Starting phenix.real_space_refine
on Fri Aug 22 21:32:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wg8_37505/08_2025/8wg8_37505.cif"
  }
  resolution = 2.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.017
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      50      5.16       5
     C    5114      2.51       5
     N    1412      2.21       5
     O    1467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8043
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1901
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2577
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 420
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 964
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2050
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 257}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "E"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 131
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 1.52, per 1000 atoms: 0.19
  Number of scatterers: 8043
  At special positions: 0
  Unit cell: (79.254, 93.177, 131.733, 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      50     16.00
     O    1467      8.00
     N    1412      7.00
     C    5114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 256.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1946

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      39.8% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.587A  pdb=" N   LYS A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.539A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 270
      removed outlier: 3.740A  pdb=" N   GLU A 266 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 4.211A  pdb=" N   THR A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 4.123A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.767A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.199A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.502A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.657A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 165
      removed outlier: 3.544A  pdb=" N   THR R 146 " --> pdb=" O   GLN R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 202
    Processing helix  chain 'R' and resid 221 through 253
      removed outlier: 3.614A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 272
    Processing helix  chain 'R' and resid 273 through 290
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 304 through 336
      removed outlier: 3.632A  pdb=" N   ARG R 308 " --> pdb=" O   TRP R 304 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE R 309 " --> pdb=" O   TRP R 305 " (cutoff:3.500A)
      Proline residue:  R 310  - end of helix
      removed outlier: 3.746A  pdb=" N   ARG R 336 " --> pdb=" O   LYS R 332 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 343 through 355
      removed outlier: 3.911A  pdb=" N   SER R 350 " --> pdb=" O   ARG R 346 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 367
    Processing helix  chain 'R' and resid 375 through 382
    Processing helix  chain 'R' and resid 384 through 402
      removed outlier: 3.503A  pdb=" N   SER R 389 " --> pdb=" O   ASP R 385 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   SER R 390 " --> pdb=" O   LEU R 386 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 419
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.663A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.779A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.583A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.042A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.835A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.293A  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: 4.220A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.834A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.762A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.878A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL N 124 " --> pdb=" O   ALA N  92 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1595
        1.33 -     1.45: 2032
        1.45 -     1.57: 4510
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8207
  Sorted by residual:
  bond pdb=" CA  PHE A 279 "
       pdb=" C   PHE A 279 "
    ideal  model  delta    sigma   weight residual
    1.523  1.565 -0.043 1.00e-02 1.00e+04 1.81e+01
  bond pdb=" C   PHE A 279 "
       pdb=" N   PRO A 280 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 1.19e-02 7.06e+03 1.40e+01
  bond pdb=" CA  ARG A 309 "
       pdb=" C   ARG A 309 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.047 1.27e-02 6.20e+03 1.39e+01
  bond pdb=" CA  CYS N  99 "
       pdb=" C   CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.522  1.492  0.030 9.10e-03 1.21e+04 1.12e+01
  bond pdb=" CA  PHE A 223 "
       pdb=" C   PHE A 223 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.036 1.17e-02 7.31e+03 9.29e+00
  ... (remaining 8202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 10888
        2.00 -     3.99: 200
        3.99 -     5.99: 26
        5.99 -     7.98: 5
        7.98 -     9.98: 3
  Bond angle restraints: 11122
  Sorted by residual:
  angle pdb=" N   GLN A  52 "
        pdb=" CA  GLN A  52 "
        pdb=" C   GLN A  52 "
      ideal   model   delta    sigma   weight residual
     111.40  101.42    9.98 1.22e+00 6.72e-01 6.69e+01
  angle pdb=" N   ARG A  54 "
        pdb=" CA  ARG A  54 "
        pdb=" C   ARG A  54 "
      ideal   model   delta    sigma   weight residual
     113.88  106.43    7.45 1.23e+00 6.61e-01 3.67e+01
  angle pdb=" N   GLN A  24 "
        pdb=" CA  GLN A  24 "
        pdb=" C   GLN A  24 "
      ideal   model   delta    sigma   weight residual
     113.12  106.03    7.09 1.25e+00 6.40e-01 3.22e+01
  angle pdb=" N   TYR N 115 "
        pdb=" CA  TYR N 115 "
        pdb=" C   TYR N 115 "
      ideal   model   delta    sigma   weight residual
     109.24  100.38    8.86 1.63e+00 3.76e-01 2.95e+01
  angle pdb=" N   CYS N  99 "
        pdb=" CA  CYS N  99 "
        pdb=" C   CYS N  99 "
      ideal   model   delta    sigma   weight residual
     109.48  100.09    9.39 1.75e+00 3.27e-01 2.88e+01
  ... (remaining 11117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4425
       17.84 -    35.67: 349
       35.67 -    53.51: 69
       53.51 -    71.34: 18
       71.34 -    89.18: 8
  Dihedral angle restraints: 4869
    sinusoidal: 1864
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" SG  CYS R 294 "
           pdb=" CB  CYS R 294 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.27   86.27     1      1.00e+01 1.00e-02 8.98e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.80   51.80     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CA  ASP B 246 "
           pdb=" CB  ASP B 246 "
           pdb=" CG  ASP B 246 "
           pdb=" OD1 ASP B 246 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.60   58.60     1      2.00e+01 2.50e-03 1.15e+01
  ... (remaining 4866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1060
       0.062 -    0.125: 172
       0.125 -    0.187: 18
       0.187 -    0.249: 10
       0.249 -    0.312: 2
  Chirality restraints: 1262
  Sorted by residual:
  chirality pdb=" CA  MET A  53 "
            pdb=" N   MET A  53 "
            pdb=" C   MET A  53 "
            pdb=" CB  MET A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  TYR N 117 "
            pdb=" N   TYR N 117 "
            pdb=" C   TYR N 117 "
            pdb=" CB  TYR N 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  ASP A 310 "
            pdb=" N   ASP A 310 "
            pdb=" C   ASP A 310 "
            pdb=" CB  ASP A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1259 not shown)

  Planarity restraints: 1415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS N  99 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.96e+00
        pdb=" N   PRO N 100 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO N 100 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO N 100 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 306 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   TYR A 306 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   TYR A 306 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 307 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 212 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ILE A 212 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ILE A 212 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN A 213 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1412 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 351
        2.72 -     3.26: 7968
        3.26 -     3.81: 13145
        3.81 -     4.35: 16159
        4.35 -     4.90: 27492
  Nonbonded interactions: 65115
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OD2 ASP A  26 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.228 3.040
  ... (remaining 65110 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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.070
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
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      :  0.005   0.047   8210  Z= 0.308
  Angle     :  0.684   9.979  11128  Z= 0.429
  Chirality :  0.049   0.312   1262
  Planarity :  0.004   0.061   1415
  Dihedral  : 13.928  89.180   2914
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  1.89 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.27), residues: 1017
  helix:  1.37 (0.28), residues: 387
  sheet: -0.27 (0.33), residues: 221
  loop : -0.92 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 250 
 TYR   0.021   0.001   TYR B  59 
 PHE   0.027   0.002   PHE A 189 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8207)
  covalent geometry    : angle       0.68400 (11122)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       1.10333 (    6)
  hydrogen bonds       : bond        0.15298 (  392)
  hydrogen bonds       : angle       5.97624 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: B  246 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (t0)
REVERT: N   17 SER cc_start: 0.8150 (m) cc_final: 0.7638 (t)
REVERT: R  287 CYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7433 (t)
REVERT: R  290 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6009 (tm-30)
REVERT: R  293 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6109 (pp30)
REVERT: R  410 GLU cc_start: 0.8887 (tp30) cc_final: 0.8551 (tp30)
  outliers start: 18
  outliers final: 3
  residues processed: 181
  average time/residue: 0.5786
  time to fit residues: 110.2344
Evaluate side-chains
  133 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  290 GLU
Chi-restraints excluded: chain R residue  293 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
A 261 GLN
A 354 HIS
A 357 GLN
B  44 GLN
N  31 ASN
N  35 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.118343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.084570 restraints weight = 13727.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 3.18
r_work: 0.3048 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8210  Z= 0.124
  Angle     :  0.572   9.036  11128  Z= 0.297
  Chirality :  0.041   0.143   1262
  Planarity :  0.004   0.043   1415
  Dihedral  :  6.281  84.744   1136
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.82 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.27), residues: 1017
  helix:  1.69 (0.28), residues: 391
  sheet: -0.04 (0.33), residues: 224
  loop : -0.98 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 250 
 TYR   0.017   0.001   TYR R 145 
 PHE   0.011   0.001   PHE A 189 
 TRP   0.023   0.001   TRP R 282 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8207)
  covalent geometry    : angle       0.57079 (11122)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       1.38182 (    6)
  hydrogen bonds       : bond        0.03935 (  392)
  hydrogen bonds       : angle       4.46430 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8250 (mm-30)
REVERT: A  311 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7266 (mp0)
REVERT: B  127 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8729 (mmtm)
REVERT: B  217 MET cc_start: 0.8912 (pmm) cc_final: 0.8556 (pmm)
REVERT: G   21 MET cc_start: 0.7563 (mpp) cc_final: 0.7343 (mpp)
REVERT: N   17 SER cc_start: 0.8065 (m) cc_final: 0.7854 (m)
REVERT: N   38 ARG cc_start: 0.8606 (mtm180) cc_final: 0.8273 (ptm-80)
REVERT: N   46 GLU cc_start: 0.8221 (pt0) cc_final: 0.7557 (pm20)
REVERT: N   53 GLN cc_start: 0.8193 (mp10) cc_final: 0.7929 (mp10)
REVERT: R  231 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6976 (ttp)
REVERT: R  290 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5621 (tm-30)
REVERT: R  293 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6556 (pp30)
REVERT: R  408 GLN cc_start: 0.8917 (mt0) cc_final: 0.8621 (mt0)
REVERT: R  410 GLU cc_start: 0.9069 (tp30) cc_final: 0.8681 (tp30)
  outliers start: 18
  outliers final: 9
  residues processed: 147
  average time/residue: 0.5667
  time to fit residues: 87.9753
Evaluate side-chains
  140 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   45 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  290 GLU
Chi-restraints excluded: chain R residue  293 GLN
Chi-restraints excluded: chain R residue  385 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
R 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084431 restraints weight = 14114.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 3.13
r_work: 0.3031 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8210  Z= 0.162
  Angle     :  0.563  12.232  11128  Z= 0.293
  Chirality :  0.041   0.143   1262
  Planarity :  0.004   0.044   1415
  Dihedral  :  5.725  88.861   1131
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.36 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.27), residues: 1017
  helix:  1.81 (0.28), residues: 392
  sheet:  0.03 (0.33), residues: 215
  loop : -0.93 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 247 
 TYR   0.016   0.001   TYR R 145 
 PHE   0.016   0.001   PHE A 185 
 TRP   0.020   0.001   TRP R 282 
 HIS   0.007   0.001   HIS R 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8207)
  covalent geometry    : angle       0.56234 (11122)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       1.39997 (    6)
  hydrogen bonds       : bond        0.04002 (  392)
  hydrogen bonds       : angle       4.28661 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7282 (mp0)
REVERT: B   59 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7971 (m-80)
REVERT: B  127 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8757 (mmtm)
REVERT: B  217 MET cc_start: 0.8876 (pmm) cc_final: 0.8420 (pmm)
REVERT: G   21 MET cc_start: 0.7659 (mpp) cc_final: 0.7441 (mpp)
REVERT: N   38 ARG cc_start: 0.8685 (mtm180) cc_final: 0.7894 (mtm180)
REVERT: N   46 GLU cc_start: 0.8264 (pt0) cc_final: 0.7652 (pm20)
REVERT: N   53 GLN cc_start: 0.8192 (mp10) cc_final: 0.7875 (mp10)
REVERT: R  142 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7898 (mm110)
REVERT: R  231 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6929 (ttp)
REVERT: R  408 GLN cc_start: 0.8924 (mt0) cc_final: 0.8629 (mt0)
REVERT: R  410 GLU cc_start: 0.9071 (tp30) cc_final: 0.8715 (tp30)
  outliers start: 26
  outliers final: 13
  residues processed: 145
  average time/residue: 0.5688
  time to fit residues: 87.1553
Evaluate side-chains
  137 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 79 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.084403 restraints weight = 14472.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.21
r_work: 0.3042 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8210  Z= 0.136
  Angle     :  0.558  12.157  11128  Z= 0.290
  Chirality :  0.040   0.133   1262
  Planarity :  0.003   0.044   1415
  Dihedral  :  4.227  39.869   1124
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.13 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 1017
  helix:  1.91 (0.28), residues: 392
  sheet:  0.07 (0.34), residues: 209
  loop : -0.89 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 247 
 TYR   0.013   0.001   TYR R 145 
 PHE   0.013   0.001   PHE A 185 
 TRP   0.019   0.001   TRP R 282 
 HIS   0.003   0.001   HIS R 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8207)
  covalent geometry    : angle       0.55713 (11122)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       1.19052 (    6)
  hydrogen bonds       : bond        0.03770 (  392)
  hydrogen bonds       : angle       4.15577 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7518 (mp0)
REVERT: A  337 GLU cc_start: 0.7725 (pm20) cc_final: 0.7506 (pm20)
REVERT: B   47 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8890 (t)
REVERT: B   59 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8006 (m-80)
REVERT: B  161 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.9050 (p)
REVERT: B  217 MET cc_start: 0.8942 (pmm) cc_final: 0.8473 (pmm)
REVERT: N   53 GLN cc_start: 0.8303 (mp10) cc_final: 0.8002 (mp10)
REVERT: R  142 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7872 (mm110)
REVERT: R  231 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7075 (ttp)
REVERT: R  405 LYS cc_start: 0.9253 (tppt) cc_final: 0.9041 (tppt)
REVERT: R  408 GLN cc_start: 0.8926 (mt0) cc_final: 0.8517 (mt0)
REVERT: R  410 GLU cc_start: 0.9052 (tp30) cc_final: 0.8719 (tp30)
  outliers start: 25
  outliers final: 11
  residues processed: 148
  average time/residue: 0.5522
  time to fit residues: 86.3607
Evaluate side-chains
  140 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   45 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
B  44 GLN
R 238 ASN
R 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.083519 restraints weight = 14245.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 3.16
r_work: 0.3028 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8210  Z= 0.152
  Angle     :  0.573  11.762  11128  Z= 0.296
  Chirality :  0.041   0.140   1262
  Planarity :  0.003   0.044   1415
  Dihedral  :  4.283  42.368   1124
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.95 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.27), residues: 1017
  helix:  1.93 (0.28), residues: 392
  sheet:  0.13 (0.34), residues: 209
  loop : -0.89 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 247 
 TYR   0.020   0.001   TYR R 145 
 PHE   0.014   0.001   PHE A 185 
 TRP   0.022   0.001   TRP R 282 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8207)
  covalent geometry    : angle       0.57280 (11122)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       1.20834 (    6)
  hydrogen bonds       : bond        0.03858 (  392)
  hydrogen bonds       : angle       4.12160 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  337 GLU cc_start: 0.7801 (pm20) cc_final: 0.7503 (pm20)
REVERT: B   47 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8896 (t)
REVERT: B   59 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8065 (m-80)
REVERT: B  161 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.9080 (p)
REVERT: B  188 MET cc_start: 0.9158 (mmp) cc_final: 0.8639 (mmm)
REVERT: B  217 MET cc_start: 0.8942 (pmm) cc_final: 0.8452 (pmm)
REVERT: G   21 MET cc_start: 0.7790 (mpp) cc_final: 0.7329 (mpp)
REVERT: N   38 ARG cc_start: 0.8788 (mtm180) cc_final: 0.8229 (ptt90)
REVERT: N   46 GLU cc_start: 0.8326 (pt0) cc_final: 0.7776 (pm20)
REVERT: N   53 GLN cc_start: 0.8309 (mp10) cc_final: 0.7997 (mp10)
REVERT: R  231 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7126 (ttp)
REVERT: R  405 LYS cc_start: 0.9255 (tppt) cc_final: 0.8990 (tppt)
REVERT: R  408 GLN cc_start: 0.8934 (mt0) cc_final: 0.8488 (mt0)
REVERT: R  410 GLU cc_start: 0.9050 (tp30) cc_final: 0.8673 (tp30)
  outliers start: 33
  outliers final: 17
  residues processed: 150
  average time/residue: 0.5441
  time to fit residues: 86.7741
Evaluate side-chains
  146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  357 LEU
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0770
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.115400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083458 restraints weight = 14193.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.15
r_work: 0.3023 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8210  Z= 0.157
  Angle     :  0.600  14.060  11128  Z= 0.307
  Chirality :  0.042   0.150   1262
  Planarity :  0.003   0.049   1415
  Dihedral  :  4.324  45.167   1124
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 20.19 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 1017
  helix:  1.98 (0.28), residues: 392
  sheet:  0.14 (0.34), residues: 209
  loop : -0.90 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 247 
 TYR   0.014   0.001   TYR R 145 
 PHE   0.014   0.001   PHE A 185 
 TRP   0.024   0.001   TRP R 282 
 HIS   0.006   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8207)
  covalent geometry    : angle       0.59944 (11122)
  SS BOND              : bond        0.00154 (    3)
  SS BOND              : angle       1.24756 (    6)
  hydrogen bonds       : bond        0.03849 (  392)
  hydrogen bonds       : angle       4.08368 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  337 GLU cc_start: 0.7852 (pm20) cc_final: 0.7533 (pm20)
REVERT: B   32 GLN cc_start: 0.8707 (mt0) cc_final: 0.8479 (mt0)
REVERT: B   47 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8904 (t)
REVERT: B   59 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8108 (m-80)
REVERT: B  188 MET cc_start: 0.9143 (mmp) cc_final: 0.8764 (mmm)
REVERT: B  217 MET cc_start: 0.8963 (pmm) cc_final: 0.8577 (pmm)
REVERT: G   21 MET cc_start: 0.7814 (mpp) cc_final: 0.7341 (mpp)
REVERT: N   46 GLU cc_start: 0.8350 (pt0) cc_final: 0.8134 (pt0)
REVERT: N   53 GLN cc_start: 0.8303 (mp10) cc_final: 0.7992 (mp10)
REVERT: R  231 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7134 (mtm)
REVERT: R  405 LYS cc_start: 0.9240 (tppt) cc_final: 0.8973 (tppt)
REVERT: R  408 GLN cc_start: 0.8932 (mt0) cc_final: 0.8523 (mt0)
REVERT: R  410 GLU cc_start: 0.8958 (tp30) cc_final: 0.8618 (tp30)
  outliers start: 35
  outliers final: 18
  residues processed: 150
  average time/residue: 0.4889
  time to fit residues: 77.9747
Evaluate side-chains
  145 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  357 LEU
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 65 optimal weight:    0.2980
   chunk 39 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN
R 177 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.115972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.084060 restraints weight = 14262.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 3.17
r_work: 0.3053 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8210  Z= 0.135
  Angle     :  0.597  14.018  11128  Z= 0.306
  Chirality :  0.041   0.176   1262
  Planarity :  0.003   0.054   1415
  Dihedral  :  4.292  45.281   1124
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.72 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.27), residues: 1017
  helix:  2.11 (0.28), residues: 386
  sheet:  0.16 (0.34), residues: 209
  loop : -0.94 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 247 
 TYR   0.019   0.001   TYR R 145 
 PHE   0.014   0.001   PHE A 185 
 TRP   0.030   0.001   TRP R 282 
 HIS   0.005   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8207)
  covalent geometry    : angle       0.59640 (11122)
  SS BOND              : bond        0.00177 (    3)
  SS BOND              : angle       1.10234 (    6)
  hydrogen bonds       : bond        0.03709 (  392)
  hydrogen bonds       : angle       4.00643 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASP cc_start: 0.8846 (t0) cc_final: 0.8614 (t0)
REVERT: A  337 GLU cc_start: 0.7811 (pm20) cc_final: 0.7463 (pm20)
REVERT: B   32 GLN cc_start: 0.8724 (mt0) cc_final: 0.8467 (mt0)
REVERT: B   47 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8869 (t)
REVERT: B   59 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8063 (m-80)
REVERT: B  188 MET cc_start: 0.9061 (mmp) cc_final: 0.8658 (mmm)
REVERT: B  217 MET cc_start: 0.8907 (pmm) cc_final: 0.8504 (pmm)
REVERT: G   21 MET cc_start: 0.7750 (mpp) cc_final: 0.7290 (mpp)
REVERT: N   53 GLN cc_start: 0.8287 (mp10) cc_final: 0.7983 (mp10)
REVERT: R  231 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7217 (mtm)
REVERT: R  357 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7154 (pp)
REVERT: R  405 LYS cc_start: 0.9237 (tppt) cc_final: 0.8949 (tppt)
REVERT: R  408 GLN cc_start: 0.8898 (mt0) cc_final: 0.8492 (mt0)
  outliers start: 28
  outliers final: 16
  residues processed: 144
  average time/residue: 0.5660
  time to fit residues: 86.4829
Evaluate side-chains
  142 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  357 LEU
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0050
   chunk 62 optimal weight:    0.0870
   chunk 37 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.3772

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN
R 238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.085218 restraints weight = 14049.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 3.14
r_work: 0.3046 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8210  Z= 0.119
  Angle     :  0.601  14.070  11128  Z= 0.309
  Chirality :  0.041   0.176   1262
  Planarity :  0.003   0.059   1415
  Dihedral  :  4.217  44.085   1124
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.49 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.27), residues: 1017
  helix:  2.17 (0.28), residues: 386
  sheet:  0.13 (0.34), residues: 210
  loop : -0.91 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 247 
 TYR   0.015   0.001   TYR R 145 
 PHE   0.015   0.001   PHE E   5 
 TRP   0.035   0.001   TRP R 282 
 HIS   0.004   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8207)
  covalent geometry    : angle       0.60120 (11122)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.90528 (    6)
  hydrogen bonds       : bond        0.03532 (  392)
  hydrogen bonds       : angle       3.97083 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASP cc_start: 0.8850 (t0) cc_final: 0.8637 (t0)
REVERT: A  337 GLU cc_start: 0.7981 (pm20) cc_final: 0.7652 (pm20)
REVERT: B   32 GLN cc_start: 0.8728 (mt0) cc_final: 0.8478 (mt0)
REVERT: B   47 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8902 (t)
REVERT: B   59 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8085 (m-80)
REVERT: B  188 MET cc_start: 0.9038 (mmp) cc_final: 0.8509 (mmm)
REVERT: B  217 MET cc_start: 0.8940 (pmm) cc_final: 0.8551 (pmm)
REVERT: G   21 MET cc_start: 0.7738 (tpp) cc_final: 0.7288 (mpp)
REVERT: N   53 GLN cc_start: 0.8315 (mp10) cc_final: 0.8006 (mp10)
REVERT: N   70 ILE cc_start: 0.8888 (tt) cc_final: 0.8511 (pp)
REVERT: N   87 LYS cc_start: 0.8214 (mttm) cc_final: 0.7952 (mttp)
REVERT: R  231 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7243 (mtm)
REVERT: R  408 GLN cc_start: 0.8876 (mt0) cc_final: 0.8529 (mt0)
  outliers start: 20
  outliers final: 14
  residues processed: 142
  average time/residue: 0.5490
  time to fit residues: 82.5348
Evaluate side-chains
  145 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 57 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0020
   chunk 73 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.116651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.083202 restraints weight = 13735.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 3.12
r_work: 0.3010 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8210  Z= 0.122
  Angle     :  0.609  14.137  11128  Z= 0.310
  Chirality :  0.041   0.181   1262
  Planarity :  0.003   0.058   1415
  Dihedral  :  4.183  44.150   1124
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.73 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.27), residues: 1017
  helix:  2.15 (0.28), residues: 386
  sheet:  0.17 (0.34), residues: 210
  loop : -0.88 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 247 
 TYR   0.016   0.001   TYR R 145 
 PHE   0.016   0.001   PHE E   5 
 TRP   0.032   0.001   TRP R 282 
 HIS   0.004   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8207)
  covalent geometry    : angle       0.60845 (11122)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       0.84906 (    6)
  hydrogen bonds       : bond        0.03490 (  392)
  hydrogen bonds       : angle       3.91940 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASP cc_start: 0.8846 (t0) cc_final: 0.8643 (t0)
REVERT: A  337 GLU cc_start: 0.7941 (pm20) cc_final: 0.7607 (pm20)
REVERT: B   32 GLN cc_start: 0.8747 (mt0) cc_final: 0.8503 (mt0)
REVERT: B   47 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8882 (t)
REVERT: B   59 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8018 (m-80)
REVERT: B  188 MET cc_start: 0.8958 (mmp) cc_final: 0.8421 (mmm)
REVERT: B  217 MET cc_start: 0.8929 (pmm) cc_final: 0.8528 (pmm)
REVERT: G   21 MET cc_start: 0.7735 (tpp) cc_final: 0.7271 (mpp)
REVERT: N   53 GLN cc_start: 0.8261 (mp10) cc_final: 0.7954 (mp10)
REVERT: N   70 ILE cc_start: 0.8868 (tt) cc_final: 0.8513 (pp)
REVERT: N   87 LYS cc_start: 0.8213 (mttm) cc_final: 0.7937 (mttm)
REVERT: R  142 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7852 (mm110)
REVERT: R  166 LEU cc_start: 0.8082 (mt) cc_final: 0.7805 (tm)
REVERT: R  231 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7178 (mtm)
REVERT: R  408 GLN cc_start: 0.8894 (mt0) cc_final: 0.8636 (mt0)
  outliers start: 21
  outliers final: 15
  residues processed: 143
  average time/residue: 0.5709
  time to fit residues: 86.5220
Evaluate side-chains
  146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0980
   chunk 13 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  84 ASN
R 238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.084722 restraints weight = 14082.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 3.15
r_work: 0.3034 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8210  Z= 0.142
  Angle     :  0.632  14.260  11128  Z= 0.323
  Chirality :  0.041   0.180   1262
  Planarity :  0.004   0.062   1415
  Dihedral  :  4.243  45.223   1124
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.73 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.27), residues: 1017
  helix:  2.16 (0.28), residues: 386
  sheet:  0.19 (0.34), residues: 210
  loop : -0.88 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 247 
 TYR   0.016   0.001   TYR R 138 
 PHE   0.016   0.001   PHE E   5 
 TRP   0.034   0.001   TRP R 282 
 HIS   0.005   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8207)
  covalent geometry    : angle       0.63198 (11122)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       0.91027 (    6)
  hydrogen bonds       : bond        0.03573 (  392)
  hydrogen bonds       : angle       3.93241 ( 1113)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASP cc_start: 0.8858 (t0) cc_final: 0.8646 (t0)
REVERT: A  337 GLU cc_start: 0.7944 (pm20) cc_final: 0.7552 (pm20)
REVERT: B   32 GLN cc_start: 0.8795 (mt0) cc_final: 0.8539 (mt0)
REVERT: B   47 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8920 (t)
REVERT: B   59 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8091 (m-80)
REVERT: B  188 MET cc_start: 0.9021 (mmp) cc_final: 0.8511 (mmm)
REVERT: B  217 MET cc_start: 0.8934 (pmm) cc_final: 0.8533 (pmm)
REVERT: G   21 MET cc_start: 0.7657 (tpp) cc_final: 0.7226 (mpp)
REVERT: N   53 GLN cc_start: 0.8336 (mp10) cc_final: 0.8018 (mp10)
REVERT: N   70 ILE cc_start: 0.8885 (tt) cc_final: 0.8523 (pp)
REVERT: N   87 LYS cc_start: 0.8290 (mttm) cc_final: 0.7985 (mttp)
REVERT: R  166 LEU cc_start: 0.7117 (mt) cc_final: 0.6764 (tp)
REVERT: R  195 ASP cc_start: 0.9246 (t0) cc_final: 0.8818 (t0)
REVERT: R  231 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7250 (mtm)
REVERT: R  408 GLN cc_start: 0.8906 (mt0) cc_final: 0.8661 (mt0)
  outliers start: 22
  outliers final: 18
  residues processed: 141
  average time/residue: 0.5867
  time to fit residues: 87.6339
Evaluate side-chains
  147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  189 SER
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0010
   chunk 48 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.4724

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.117026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.085460 restraints weight = 14091.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 3.15
r_work: 0.3065 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8210  Z= 0.125
  Angle     :  0.625  13.595  11128  Z= 0.318
  Chirality :  0.041   0.180   1262
  Planarity :  0.003   0.059   1415
  Dihedral  :  4.214  44.570   1124
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 23.49 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.27), residues: 1017
  helix:  2.24 (0.27), residues: 384
  sheet:  0.19 (0.34), residues: 210
  loop : -0.84 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 247 
 TYR   0.015   0.001   TYR R 138 
 PHE   0.017   0.001   PHE E   5 
 TRP   0.036   0.001   TRP R 282 
 HIS   0.004   0.000   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8207)
  covalent geometry    : angle       0.62477 (11122)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.80049 (    6)
  hydrogen bonds       : bond        0.03480 (  392)
  hydrogen bonds       : angle       3.90772 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2877.47 seconds
wall clock time: 49 minutes 45.11 seconds (2985.11 seconds total)