Starting phenix.real_space_refine
on Thu Mar 13 04:55:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wss_37823/03_2025/8wss_37823.cif"
  }
  resolution = 3.01
  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=   0.002
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      67      5.16       5
     C    5624      2.51       5
     N    1489      2.21       5
     O    1617      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8797
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1749
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2560
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "G"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 401
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "H"
      Number of atoms: 1720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1720
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "L"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 149
          Classifications: {'peptide': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
    Chain: "R"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2218
          Classifications: {'peptide': 283}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 267}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 5.38, per 1000 atoms: 0.61
  Number of scatterers: 8797
  At special positions: 0
  Unit cell: (86.52, 122.776, 131.016, 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      67     16.00
     O    1617      8.00
     N    1489      7.00
     C    5624      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L   7 " - pdb=" SG  CYS L  16 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 185 " - pdb=" SG  CYS R 263 " distance=2.08

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 15 sheets defined
      36.9% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.911A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.623A  pdb=" N   LYS A  51 " --> pdb=" O   ASN A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.108A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.691A  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 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.959A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.672A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.656A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.944A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 221 through 225
      removed outlier: 3.761A  pdb=" N   ASP H 224 " --> pdb=" O   GLU H 221 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL H 225 " --> pdb=" O   ALA H 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 221 through 225'
    Processing helix  chain 'R' and resid 111 through 138
    Processing helix  chain 'R' and resid 145 through 173
      Proline residue:  R 166  - end of helix
    Processing helix  chain 'R' and resid 181 through 216
      removed outlier: 3.806A  pdb=" N   THR R 186 " --> pdb=" O   GLU R 182 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU R 187 " --> pdb=" O   THR R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 222
    Processing helix  chain 'R' and resid 224 through 250
      removed outlier: 4.050A  pdb=" N   VAL R 228 " --> pdb=" O   ARG R 224 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU R 231 " --> pdb=" O   SER R 227 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 272 through 286
      removed outlier: 4.262A  pdb=" N   TRP R 276 " --> pdb=" O   THR R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 303
    Processing helix  chain 'R' and resid 313 through 348
      removed outlier: 3.675A  pdb=" N   CYS R 337 " --> pdb=" O   VAL R 333 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TRP R 338 " --> pdb=" O   PHE R 334 " (cutoff:3.500A)
      Proline residue:  R 340  - end of helix
    Processing helix  chain 'R' and resid 349 through 351
      No H-bonds generated for 'chain 'R' and resid 349 through 351'
    Processing helix  chain 'R' and resid 357 through 384
      Proline residue:  R 377  - end of helix
    Processing helix  chain 'R' and resid 384 through 392
      removed outlier: 3.677A  pdb=" N   VAL R 392 " --> pdb=" O   ARG R 388 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.887A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.642A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.556A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.536A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.965A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.798A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.482A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.580A  pdb=" N   THR H 118 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 60
      removed outlier: 6.659A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 147 through 149
      removed outlier: 3.541A  pdb=" N   GLU H 247 " --> pdb=" O   VAL H 148 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TRP H 177 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 161
    Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 9
    Processing sheet with id=AB6, first strand: chain 'R' and resid 253 through 254

    433 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.41

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2812
        1.34 -     1.46: 2220
        1.46 -     1.58: 3854
        1.58 -     1.70: 0
        1.70 -     1.82: 97
  Bond restraints: 8983
  Sorted by residual:
  bond pdb=" N   ARG L  11 "
       pdb=" CA  ARG L  11 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.37e-02 5.33e+03 7.13e+00
  bond pdb=" N   MET R 165 "
       pdb=" CA  MET R 165 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.04e-02 9.25e+03 5.24e+00
  bond pdb=" N   ASN R 194 "
       pdb=" CA  ASN R 194 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.97e+00
  bond pdb=" N   SER R 195 "
       pdb=" CA  SER R 195 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.90e+00
  bond pdb=" N   GLN R 196 "
       pdb=" CA  GLN R 196 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.56e+00
  ... (remaining 8978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 11911
        1.22 -     2.43: 212
        2.43 -     3.65: 49
        3.65 -     4.87: 12
        4.87 -     6.08: 5
  Bond angle restraints: 12189
  Sorted by residual:
  angle pdb=" CA  GLY H  10 "
        pdb=" C   GLY H  10 "
        pdb=" N   LEU H  11 "
      ideal   model   delta    sigma   weight residual
     114.23  116.73   -2.50 8.80e-01 1.29e+00 8.04e+00
  angle pdb=" N   THR R 272 "
        pdb=" CA  THR R 272 "
        pdb=" C   THR R 272 "
      ideal   model   delta    sigma   weight residual
     113.18  109.75    3.43 1.33e+00 5.65e-01 6.63e+00
  angle pdb=" O   ASN R 194 "
        pdb=" C   ASN R 194 "
        pdb=" N   SER R 195 "
      ideal   model   delta    sigma   weight residual
     122.12  124.64   -2.52 1.06e+00 8.90e-01 5.65e+00
  angle pdb=" CA  ASN R 194 "
        pdb=" C   ASN R 194 "
        pdb=" O   ASN R 194 "
      ideal   model   delta    sigma   weight residual
     120.55  118.05    2.50 1.06e+00 8.90e-01 5.58e+00
  angle pdb=" CA  GLY H  10 "
        pdb=" C   GLY H  10 "
        pdb=" O   GLY H  10 "
      ideal   model   delta    sigma   weight residual
     122.33  120.55    1.78 8.10e-01 1.52e+00 4.80e+00
  ... (remaining 12184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.91: 4952
       13.91 -    27.82: 242
       27.82 -    41.74: 87
       41.74 -    55.65: 21
       55.65 -    69.56: 2
  Dihedral angle restraints: 5304
    sinusoidal: 1992
      harmonic: 3312
  Sorted by residual:
  dihedral pdb=" CA  GLN R 196 "
           pdb=" CB  GLN R 196 "
           pdb=" CG  GLN R 196 "
           pdb=" CD  GLN R 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.57  -57.43     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" N   LEU R 284 "
           pdb=" CA  LEU R 284 "
           pdb=" CB  LEU R 284 "
           pdb=" CG  LEU R 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.25  -54.75     3      1.50e+01 4.44e-03 9.30e+00
  dihedral pdb=" CA  LYS G  46 "
           pdb=" CB  LYS G  46 "
           pdb=" CG  LYS G  46 "
           pdb=" CD  LYS G  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.41  -54.59     3      1.50e+01 4.44e-03 9.29e+00
  ... (remaining 5301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 835
       0.024 -    0.049: 318
       0.049 -    0.073: 135
       0.073 -    0.097: 66
       0.097 -    0.121: 51
  Chirality restraints: 1405
  Sorted by residual:
  chirality pdb=" CA  MET R 112 "
            pdb=" N   MET R 112 "
            pdb=" C   MET R 112 "
            pdb=" CB  MET R 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  PRO R 166 "
            pdb=" N   PRO R 166 "
            pdb=" C   PRO R 166 "
            pdb=" CB  PRO R 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.64e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 1402 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET R 112 "   -0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO R 113 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 113 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 113 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG L  14 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO L  15 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO L  15 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L  15 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "    0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO G  55 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 94
        2.65 -     3.21: 7892
        3.21 -     3.77: 13415
        3.77 -     4.34: 18204
        4.34 -     4.90: 30790
  Nonbonded interactions: 70395
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 229 "
            pdb=" CD1 LEU A 232 "
     model   vdw
     2.082 3.460
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH1 ARG H 203 "
            pdb=" OD2 ASP H 224 "
     model   vdw
     2.254 3.120
  ... (remaining 70390 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.580
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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      :  0.002   0.037   8983  Z= 0.127
  Angle     :  0.456   6.082  12189  Z= 0.259
  Chirality :  0.038   0.121   1405
  Planarity :  0.003   0.049   1532
  Dihedral  :  9.953  69.560   3157
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.53 %
    Favored  : 91.04 %
  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:  1.40 (0.26), residues: 1119
  helix:  2.57 (0.27), residues: 376
  sheet:  1.50 (0.32), residues: 273
  loop : -0.85 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 111 
 HIS   0.002   0.000   HIS R 179 
 PHE   0.007   0.001   PHE R 161 
 TYR   0.010   0.001   TYR R 275 
 ARG   0.003   0.000   ARG B 256 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 244
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7345 (mtm110)
REVERT: A   29 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7314 (ttpt)
REVERT: A  195 HIS cc_start: 0.7562 (m-70) cc_final: 0.7216 (t70)
REVERT: A  252 SER cc_start: 0.8985 (t) cc_final: 0.8691 (m)
REVERT: B   79 LEU cc_start: 0.8583 (mp) cc_final: 0.8356 (mt)
REVERT: B  239 ASN cc_start: 0.8612 (m-40) cc_final: 0.8336 (m-40)
REVERT: H  109 ASP cc_start: 0.8721 (p0) cc_final: 0.8507 (p0)
REVERT: H  221 GLU cc_start: 0.7539 (pm20) cc_final: 0.7149 (pt0)
REVERT: R  109 ASN cc_start: 0.4767 (p0) cc_final: 0.4100 (m-40)
REVERT: R  127 ASN cc_start: 0.5928 (m-40) cc_final: 0.5721 (m-40)
REVERT: R  198 THR cc_start: 0.8398 (t) cc_final: 0.8173 (m)
REVERT: R  202 ILE cc_start: 0.8040 (mm) cc_final: 0.7795 (mt)
REVERT: R  261 VAL cc_start: 0.7207 (m) cc_final: 0.6815 (p)
REVERT: R  280 TYR cc_start: 0.6684 (t80) cc_final: 0.6441 (t80)
  outliers start: 4
  outliers final: 1
  residues processed: 247
  average time/residue: 0.2426
  time to fit residues: 79.8580
Evaluate side-chains
  142 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  170 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0070
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 255 ASN
A 304 GLN
B 183 HIS
B 220 GLN
B 230 ASN
H  39 GLN
H 143 GLN
H 184 GLN
R 281 GLN
R 345 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.154452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121536 restraints weight = 10973.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.81
r_work: 0.3272 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8983  Z= 0.182
  Angle     :  0.527   6.307  12189  Z= 0.277
  Chirality :  0.042   0.157   1405
  Planarity :  0.004   0.047   1532
  Dihedral  :  3.721  37.678   1231
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 11.30 %
    Favored  : 85.39 %
  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:  1.29 (0.26), residues: 1119
  helix:  2.65 (0.27), residues: 377
  sheet:  1.47 (0.32), residues: 252
  loop : -0.99 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R 170 
 PHE   0.024   0.001   PHE R 286 
 TYR   0.012   0.001   TYR R 275 
 ARG   0.005   0.001   ARG B 129 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7319 (mtm110)
REVERT: A   29 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7233 (ttpt)
REVERT: A  195 HIS cc_start: 0.8054 (m-70) cc_final: 0.7200 (t-170)
REVERT: A  273 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7613 (mm)
REVERT: B  221 THR cc_start: 0.8912 (t) cc_final: 0.8588 (m)
REVERT: B  268 ASN cc_start: 0.7994 (t0) cc_final: 0.7702 (t0)
REVERT: H   23 SER cc_start: 0.8067 (m) cc_final: 0.7816 (t)
REVERT: H   90 ASP cc_start: 0.7923 (m-30) cc_final: 0.7698 (m-30)
REVERT: H  221 GLU cc_start: 0.7680 (pm20) cc_final: 0.7472 (pt0)
REVERT: R  109 ASN cc_start: 0.4245 (p0) cc_final: 0.3865 (m-40)
REVERT: R  112 MET cc_start: 0.5636 (pmm) cc_final: 0.5365 (pmm)
REVERT: R  183 THR cc_start: 0.6337 (p) cc_final: 0.6130 (t)
REVERT: R  198 THR cc_start: 0.8203 (t) cc_final: 0.7986 (m)
REVERT: R  202 ILE cc_start: 0.7916 (mm) cc_final: 0.7699 (mt)
REVERT: R  261 VAL cc_start: 0.6845 (m) cc_final: 0.6611 (p)
REVERT: R  280 TYR cc_start: 0.6701 (t80) cc_final: 0.6462 (t80)
REVERT: R  393 LEU cc_start: 0.0058 (OUTLIER) cc_final: -0.0331 (pp)
  outliers start: 31
  outliers final: 16
  residues processed: 181
  average time/residue: 0.2160
  time to fit residues: 53.5795
Evaluate side-chains
  155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  170 HIS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 ASN
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 61 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.148834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115220 restraints weight = 11253.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.94
r_work: 0.3174 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8983  Z= 0.177
  Angle     :  0.510   7.389  12189  Z= 0.266
  Chirality :  0.041   0.151   1405
  Planarity :  0.003   0.045   1532
  Dihedral  :  3.803  37.381   1231
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.11 %
    Favored  : 84.22 %
  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:  1.18 (0.26), residues: 1119
  helix:  2.51 (0.27), residues: 384
  sheet:  1.42 (0.32), residues: 258
  loop : -1.12 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 170 
 PHE   0.010   0.001   PHE R 286 
 TYR   0.012   0.001   TYR R 275 
 ARG   0.005   0.000   ARG B  19 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7370 (mtm110)
REVERT: A   29 LYS cc_start: 0.7533 (ttmm) cc_final: 0.7185 (ttpt)
REVERT: A  195 HIS cc_start: 0.8096 (m-70) cc_final: 0.7144 (t70)
REVERT: A  249 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8492 (tt)
REVERT: A  252 SER cc_start: 0.8946 (t) cc_final: 0.8641 (m)
REVERT: B  146 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: B  221 THR cc_start: 0.8882 (t) cc_final: 0.8577 (m)
REVERT: B  268 ASN cc_start: 0.7942 (t0) cc_final: 0.7674 (t0)
REVERT: G   15 LEU cc_start: 0.7859 (tt) cc_final: 0.7591 (tp)
REVERT: H   90 ASP cc_start: 0.8178 (m-30) cc_final: 0.7951 (m-30)
REVERT: H  193 MET cc_start: 0.8288 (ptt) cc_final: 0.8060 (ttp)
REVERT: R  109 ASN cc_start: 0.4296 (p0) cc_final: 0.3905 (m-40)
REVERT: R  112 MET cc_start: 0.5471 (pmm) cc_final: 0.5168 (pmm)
REVERT: R  165 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7158 (ttt)
REVERT: R  198 THR cc_start: 0.8251 (t) cc_final: 0.8023 (m)
REVERT: R  202 ILE cc_start: 0.8011 (mm) cc_final: 0.7805 (mt)
REVERT: R  280 TYR cc_start: 0.6706 (t80) cc_final: 0.6477 (t80)
REVERT: R  303 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.6796 (tpt170)
REVERT: R  383 LEU cc_start: 0.8154 (mm) cc_final: 0.7758 (mm)
  outliers start: 25
  outliers final: 15
  residues processed: 159
  average time/residue: 0.2448
  time to fit residues: 53.4038
Evaluate side-chains
  150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  211 THR
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  269 ASN
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
R 171 GLN
R 348 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.143357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108602 restraints weight = 11157.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.92
r_work: 0.3073 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8983  Z= 0.269
  Angle     :  0.574   8.013  12189  Z= 0.299
  Chirality :  0.043   0.164   1405
  Planarity :  0.004   0.043   1532
  Dihedral  :  4.099  18.797   1229
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.95 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 13.54 %
    Favored  : 82.62 %
  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:  0.92 (0.25), residues: 1119
  helix:  2.37 (0.27), residues: 384
  sheet:  1.14 (0.32), residues: 260
  loop : -1.26 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 170 
 PHE   0.013   0.002   PHE H 178 
 TYR   0.014   0.002   TYR R 275 
 ARG   0.005   0.001   ARG B 129 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7733 (ttm170)
REVERT: A   29 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7337 (ttpt)
REVERT: A  195 HIS cc_start: 0.8168 (m-70) cc_final: 0.7178 (t-90)
REVERT: A  249 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8429 (tt)
REVERT: A  252 SER cc_start: 0.8956 (t) cc_final: 0.8684 (m)
REVERT: A  276 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6663 (tt0)
REVERT: A  305 CYS cc_start: 0.8054 (t) cc_final: 0.7320 (m)
REVERT: B   46 ARG cc_start: 0.8223 (mpt180) cc_final: 0.7890 (mtm-85)
REVERT: B  136 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8761 (p)
REVERT: B  146 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8188 (mp)
REVERT: B  221 THR cc_start: 0.8895 (t) cc_final: 0.8592 (m)
REVERT: B  243 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8324 (t)
REVERT: G   15 LEU cc_start: 0.7953 (tt) cc_final: 0.7724 (tp)
REVERT: R  127 ASN cc_start: 0.6800 (m-40) cc_final: 0.6394 (m110)
REVERT: R  132 PHE cc_start: 0.7406 (t80) cc_final: 0.6610 (t80)
REVERT: R  185 CYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5656 (t)
REVERT: R  187 LEU cc_start: 0.6867 (tt) cc_final: 0.6575 (mt)
REVERT: R  202 ILE cc_start: 0.8067 (mm) cc_final: 0.7786 (mt)
REVERT: R  280 TYR cc_start: 0.6834 (t80) cc_final: 0.6612 (t80)
REVERT: R  303 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.6681 (tpt170)
REVERT: R  341 TYR cc_start: 0.7639 (t80) cc_final: 0.7414 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 171
  average time/residue: 0.2334
  time to fit residues: 54.2754
Evaluate side-chains
  160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  211 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 ASN
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.143505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108950 restraints weight = 11098.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.91
r_work: 0.3075 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8983  Z= 0.210
  Angle     :  0.526   6.853  12189  Z= 0.276
  Chirality :  0.042   0.264   1405
  Planarity :  0.004   0.042   1532
  Dihedral  :  3.979  17.557   1229
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.95 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 14.07 %
    Favored  : 82.09 %
  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:  0.85 (0.25), residues: 1119
  helix:  2.36 (0.27), residues: 385
  sheet:  1.01 (0.32), residues: 260
  loop : -1.30 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 170 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.012   0.001   TYR H 191 
 ARG   0.003   0.000   ARG B 129 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7506 (mtm110)
REVERT: A   29 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7311 (ttpt)
REVERT: A  195 HIS cc_start: 0.8166 (m-70) cc_final: 0.7195 (t-170)
REVERT: A  249 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8452 (tt)
REVERT: A  252 SER cc_start: 0.8933 (t) cc_final: 0.8626 (m)
REVERT: A  276 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6704 (tt0)
REVERT: A  305 CYS cc_start: 0.8093 (t) cc_final: 0.7358 (m)
REVERT: B   46 ARG cc_start: 0.8204 (mpt180) cc_final: 0.7873 (mtm-85)
REVERT: B  136 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (p)
REVERT: B  146 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: B  221 THR cc_start: 0.8847 (t) cc_final: 0.8563 (m)
REVERT: B  243 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8331 (t)
REVERT: G   15 LEU cc_start: 0.7936 (tt) cc_final: 0.7661 (tp)
REVERT: H   23 SER cc_start: 0.8302 (m) cc_final: 0.8039 (t)
REVERT: H   38 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8085 (ttm170)
REVERT: R  132 PHE cc_start: 0.7419 (t80) cc_final: 0.6766 (t80)
REVERT: R  185 CYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5642 (t)
REVERT: R  187 LEU cc_start: 0.6858 (tt) cc_final: 0.6533 (mt)
REVERT: R  198 THR cc_start: 0.8401 (t) cc_final: 0.7996 (t)
REVERT: R  202 ILE cc_start: 0.8043 (mm) cc_final: 0.7810 (mt)
REVERT: R  303 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6627 (tpt170)
  outliers start: 36
  outliers final: 23
  residues processed: 155
  average time/residue: 0.2422
  time to fit residues: 50.1459
Evaluate side-chains
  154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  211 THR
Chi-restraints excluded: chain H residue  221 GLU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 ASN
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0030
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.144129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.109597 restraints weight = 11062.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.89
r_work: 0.3082 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8983  Z= 0.188
  Angle     :  0.515   7.000  12189  Z= 0.270
  Chirality :  0.042   0.192   1405
  Planarity :  0.003   0.041   1532
  Dihedral  :  3.881  17.307   1229
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.13 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.29 %
    Favored  : 81.77 %
  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:  0.83 (0.25), residues: 1119
  helix:  2.42 (0.27), residues: 386
  sheet:  0.90 (0.32), residues: 260
  loop : -1.33 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 170 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.012   0.001   TYR H 191 
 ARG   0.004   0.000   ARG B 129 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7550 (mtm110)
REVERT: A   29 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7313 (ttpt)
REVERT: A  195 HIS cc_start: 0.8162 (m-70) cc_final: 0.7215 (t-170)
REVERT: A  249 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8493 (tt)
REVERT: A  252 SER cc_start: 0.8934 (t) cc_final: 0.8618 (m)
REVERT: A  276 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6689 (tt0)
REVERT: A  305 CYS cc_start: 0.8090 (t) cc_final: 0.7357 (m)
REVERT: B   46 ARG cc_start: 0.8251 (mpt180) cc_final: 0.7923 (mtm-85)
REVERT: B  136 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8753 (p)
REVERT: B  146 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: B  221 THR cc_start: 0.8840 (t) cc_final: 0.8564 (m)
REVERT: B  243 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8335 (t)
REVERT: H   23 SER cc_start: 0.8293 (m) cc_final: 0.8024 (t)
REVERT: H   38 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8059 (ttm170)
REVERT: R  127 ASN cc_start: 0.6696 (m-40) cc_final: 0.6321 (m110)
REVERT: R  185 CYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5627 (t)
REVERT: R  187 LEU cc_start: 0.6954 (tt) cc_final: 0.6503 (mt)
REVERT: R  202 ILE cc_start: 0.8031 (mm) cc_final: 0.7756 (mt)
REVERT: R  303 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6681 (tpt170)
  outliers start: 37
  outliers final: 24
  residues processed: 152
  average time/residue: 0.2355
  time to fit residues: 48.8011
Evaluate side-chains
  154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  211 THR
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 ASN
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.143869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.109274 restraints weight = 11148.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.95
r_work: 0.3077 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8983  Z= 0.196
  Angle     :  0.515   6.583  12189  Z= 0.272
  Chirality :  0.041   0.198   1405
  Planarity :  0.003   0.043   1532
  Dihedral  :  3.889  17.374   1229
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.31 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.82 %
    Favored  : 81.45 %
  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:  0.87 (0.26), residues: 1119
  helix:  2.49 (0.27), residues: 385
  sheet:  0.82 (0.32), residues: 267
  loop : -1.28 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 170 
 PHE   0.010   0.001   PHE R 223 
 TYR   0.012   0.001   TYR H 191 
 ARG   0.003   0.000   ARG B 129 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7533 (mtm110)
REVERT: A   29 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7276 (ttpt)
REVERT: A  195 HIS cc_start: 0.8150 (m-70) cc_final: 0.7206 (t-170)
REVERT: A  249 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (tt)
REVERT: A  252 SER cc_start: 0.8920 (t) cc_final: 0.8606 (m)
REVERT: A  276 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6748 (tt0)
REVERT: A  305 CYS cc_start: 0.8070 (t) cc_final: 0.7345 (m)
REVERT: B   46 ARG cc_start: 0.8266 (mpt180) cc_final: 0.7941 (mtm-85)
REVERT: B  129 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7632 (mmm-85)
REVERT: B  136 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8753 (p)
REVERT: B  221 THR cc_start: 0.8836 (t) cc_final: 0.8559 (m)
REVERT: B  243 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8339 (t)
REVERT: H   23 SER cc_start: 0.8329 (m) cc_final: 0.8056 (t)
REVERT: H   38 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.8064 (ttm170)
REVERT: H  167 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8937 (tt)
REVERT: R  127 ASN cc_start: 0.6706 (m-40) cc_final: 0.6289 (m110)
REVERT: R  185 CYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5644 (t)
REVERT: R  187 LEU cc_start: 0.6918 (tt) cc_final: 0.6461 (mt)
REVERT: R  202 ILE cc_start: 0.8037 (mm) cc_final: 0.7771 (mt)
REVERT: R  303 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6594 (tpt170)
  outliers start: 35
  outliers final: 24
  residues processed: 153
  average time/residue: 0.2353
  time to fit residues: 47.9942
Evaluate side-chains
  153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  167 LEU
Chi-restraints excluded: chain H residue  211 THR
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  375 LEU
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0770
   chunk 52 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0870
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.5516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.145884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.111982 restraints weight = 11266.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.94
r_work: 0.3121 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8983  Z= 0.151
  Angle     :  0.495   7.564  12189  Z= 0.259
  Chirality :  0.041   0.201   1405
  Planarity :  0.003   0.044   1532
  Dihedral  :  3.713  17.216   1229
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.13 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.35 %
    Favored  : 81.56 %
  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:  0.93 (0.26), residues: 1119
  helix:  2.53 (0.27), residues: 385
  sheet:  0.89 (0.32), residues: 259
  loop : -1.24 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 170 
 PHE   0.011   0.001   PHE R 223 
 TYR   0.013   0.001   TYR H 191 
 ARG   0.007   0.000   ARG R 325 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.157 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7193 (ttpt)
REVERT: A  195 HIS cc_start: 0.8137 (m-70) cc_final: 0.7158 (t-170)
REVERT: A  249 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8461 (tt)
REVERT: A  252 SER cc_start: 0.8916 (t) cc_final: 0.8599 (m)
REVERT: A  276 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6785 (tt0)
REVERT: A  305 CYS cc_start: 0.8041 (t) cc_final: 0.7333 (m)
REVERT: B  129 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7624 (mmm-85)
REVERT: B  221 THR cc_start: 0.8795 (t) cc_final: 0.8523 (m)
REVERT: B  243 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8309 (t)
REVERT: H   23 SER cc_start: 0.8378 (m) cc_final: 0.8108 (t)
REVERT: H   38 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7988 (ttm170)
REVERT: H  167 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8948 (tt)
REVERT: R  185 CYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5550 (t)
REVERT: R  187 LEU cc_start: 0.6842 (tt) cc_final: 0.6430 (mt)
REVERT: R  202 ILE cc_start: 0.8043 (mm) cc_final: 0.7744 (mt)
REVERT: R  303 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.6722 (tpt170)
REVERT: R  383 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7850 (mm)
  outliers start: 29
  outliers final: 21
  residues processed: 154
  average time/residue: 0.2638
  time to fit residues: 53.8716
Evaluate side-chains
  150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  167 LEU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  375 LEU
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  383 LEU
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 89 optimal weight:    0.1980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.145002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111015 restraints weight = 11169.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.88
r_work: 0.3105 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8983  Z= 0.171
  Angle     :  0.504   6.291  12189  Z= 0.266
  Chirality :  0.041   0.211   1405
  Planarity :  0.003   0.046   1532
  Dihedral  :  3.766  17.183   1229
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.22 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.78 %
    Favored  : 81.24 %
  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:  0.89 (0.26), residues: 1119
  helix:  2.47 (0.27), residues: 385
  sheet:  0.94 (0.33), residues: 253
  loop : -1.25 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 170 
 PHE   0.010   0.001   PHE R 223 
 TYR   0.012   0.001   TYR H 191 
 ARG   0.006   0.000   ARG R 325 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7592 (ttmm) cc_final: 0.7222 (ttpt)
REVERT: A  195 HIS cc_start: 0.8154 (m-70) cc_final: 0.7179 (t-170)
REVERT: A  198 MET cc_start: 0.8752 (ttm) cc_final: 0.8461 (mtm)
REVERT: A  249 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (tt)
REVERT: A  252 SER cc_start: 0.8933 (t) cc_final: 0.8634 (m)
REVERT: A  276 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6759 (tt0)
REVERT: A  305 CYS cc_start: 0.8144 (t) cc_final: 0.7356 (m)
REVERT: B  129 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7631 (mmm-85)
REVERT: B  136 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8754 (p)
REVERT: B  221 THR cc_start: 0.8827 (t) cc_final: 0.8553 (m)
REVERT: B  243 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8313 (t)
REVERT: H    7 SER cc_start: 0.8791 (p) cc_final: 0.8560 (t)
REVERT: H   23 SER cc_start: 0.8308 (m) cc_final: 0.8050 (t)
REVERT: H   38 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8010 (ttm170)
REVERT: H  167 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (tt)
REVERT: R  127 ASN cc_start: 0.6733 (m-40) cc_final: 0.6286 (m110)
REVERT: R  185 CYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5728 (t)
REVERT: R  187 LEU cc_start: 0.6865 (tt) cc_final: 0.6453 (mt)
REVERT: R  202 ILE cc_start: 0.8019 (mm) cc_final: 0.7745 (mt)
REVERT: R  303 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.6647 (tpt170)
REVERT: R  383 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7895 (mm)
  outliers start: 28
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2328
  time to fit residues: 46.6508
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  167 LEU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  375 LEU
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  383 LEU
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
H 187 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.143900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110008 restraints weight = 11129.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.87
r_work: 0.3089 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8983  Z= 0.188
  Angle     :  0.516   6.470  12189  Z= 0.272
  Chirality :  0.042   0.216   1405
  Planarity :  0.003   0.045   1532
  Dihedral  :  3.831  17.323   1229
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.22 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.78 %
    Favored  : 81.34 %
  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:  0.88 (0.26), residues: 1119
  helix:  2.46 (0.27), residues: 385
  sheet:  0.87 (0.32), residues: 260
  loop : -1.23 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 170 
 PHE   0.011   0.001   PHE R 223 
 TYR   0.011   0.001   TYR H 191 
 ARG   0.006   0.000   ARG R 325 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7253 (ttpt)
REVERT: A  195 HIS cc_start: 0.8149 (m-70) cc_final: 0.7169 (t-170)
REVERT: A  198 MET cc_start: 0.8750 (ttm) cc_final: 0.8459 (mtm)
REVERT: A  249 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8514 (tt)
REVERT: A  252 SER cc_start: 0.8958 (t) cc_final: 0.8656 (m)
REVERT: A  276 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6766 (tt0)
REVERT: A  305 CYS cc_start: 0.8072 (t) cc_final: 0.7400 (m)
REVERT: B  129 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7629 (mmm-85)
REVERT: B  136 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8765 (p)
REVERT: B  221 THR cc_start: 0.8837 (t) cc_final: 0.8561 (m)
REVERT: B  243 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (t)
REVERT: H   23 SER cc_start: 0.8320 (m) cc_final: 0.8066 (t)
REVERT: H   38 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8047 (ttm170)
REVERT: H  167 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8974 (tt)
REVERT: R  127 ASN cc_start: 0.6788 (m-40) cc_final: 0.6307 (m110)
REVERT: R  185 CYS cc_start: 0.6282 (OUTLIER) cc_final: 0.5816 (t)
REVERT: R  187 LEU cc_start: 0.6835 (tt) cc_final: 0.6412 (mt)
REVERT: R  198 THR cc_start: 0.8345 (t) cc_final: 0.7922 (t)
REVERT: R  202 ILE cc_start: 0.8012 (mm) cc_final: 0.7744 (mt)
REVERT: R  303 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.6554 (tpt170)
  outliers start: 27
  outliers final: 19
  residues processed: 141
  average time/residue: 0.2426
  time to fit residues: 45.5840
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  167 LEU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  227 SER
Chi-restraints excluded: chain R residue  374 CYS
Chi-restraints excluded: chain R residue  375 LEU
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  393 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
H 187 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.143532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109143 restraints weight = 11201.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.91
r_work: 0.3080 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8983  Z= 0.202
  Angle     :  0.527   6.796  12189  Z= 0.279
  Chirality :  0.042   0.219   1405
  Planarity :  0.003   0.046   1532
  Dihedral  :  3.907  17.438   1229
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.46 %
    Favored  : 81.24 %
  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:  0.84 (0.26), residues: 1119
  helix:  2.42 (0.27), residues: 385
  sheet:  0.86 (0.32), residues: 260
  loop : -1.26 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 170 
 PHE   0.011   0.001   PHE R 223 
 TYR   0.011   0.001   TYR H 191 
 ARG   0.006   0.000   ARG R 325 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5525.44 seconds
wall clock time: 96 minutes 44.03 seconds (5804.03 seconds total)