Starting phenix.real_space_refine
on Tue Mar  3 21:46:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2026/7ljd_23391.map"
  }
  resolution = 3.2
  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=   0.013
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: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      2      4.86       5
     C    5468      2.51       5
     N    1447      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8518
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2269
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 10, 'TRANS': 274}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1987
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 253
          Unusual residues: {'CLR': 5, 'G4C': 1, 'LDP': 1, 'PLM': 4}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  LDP R 501 " occ=0.50
      ... (9 atoms not shown)
      pdb=" O2  LDP R 501 " occ=0.50
  Time building chain proxies: 2.49, per 1000 atoms: 0.29
  Number of scatterers: 8518
  At special positions: 0
  Unit cell: (95.316, 99.372, 121.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      56     16.00
     O    1545      8.00
     N    1447      7.00
     C    5468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03
    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

  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: 0.76
  Conformation dependent library (CDL) restraints added in 315.5 milliseconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.4% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 50
      removed outlier: 4.292A  pdb=" N   LEU R  25 " --> pdb=" O   SER R  21 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 52 through 57
      removed outlier: 4.131A  pdb=" N   LYS R  57 " --> pdb=" O   HIS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 77
      removed outlier: 3.886A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL R  73 " --> pdb=" O   SER R  69 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA R  74 " --> pdb=" O   ASP R  70 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
      removed outlier: 3.845A  pdb=" N   LYS R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 4.162A  pdb=" N   ILE R  98 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA R 101 " --> pdb=" O   ASN R  97 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 135
      removed outlier: 3.676A  pdb=" N   GLU R 132 " --> pdb=" O   PRO R 128 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG R 133 " --> pdb=" O   PHE R 129 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   MET R 135 " --> pdb=" O   TYR R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 162
      removed outlier: 4.784A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 191 through 203
      removed outlier: 3.599A  pdb=" N   ILE R 196 " --> pdb=" O   ARG R 192 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 242
    Processing helix  chain 'R' and resid 265 through 298
      removed outlier: 3.576A  pdb=" N   LEU R 274 " --> pdb=" O   VAL R 270 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 4.145A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS R 293 " --> pdb=" O   PHE R 289 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 309 through 332
      removed outlier: 3.648A  pdb=" N   TRP R 318 " --> pdb=" O   ASP R 314 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE R 319 " --> pdb=" O   VAL R 315 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'A' and resid 10 through 40
    Processing helix  chain 'A' and resid 95 through 103
      removed outlier: 3.580A  pdb=" N   GLN A  98 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A  99 " --> pdb=" O   TRP A  96 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 103 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 154
      removed outlier: 3.668A  pdb=" N   LEU A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 164
      removed outlier: 4.155A  pdb=" N   ASP A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 3.559A  pdb=" N   PHE A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.673A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.919A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 61 through 65
      removed outlier: 3.527A  pdb=" N   VAL N  64 " --> pdb=" O   THR N  61 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
      removed outlier: 6.180A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.977A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.785A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.071A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.292A  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: 6.680A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.938A  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: 3.612A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.617A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.391A  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: 6.602A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.576A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.698A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1236 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: 1.35

  Time building geometry restraints manager: 1.03 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: 2114
        1.33 -     1.45: 1750
        1.45 -     1.58: 4760
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8702
  Sorted by residual:
  bond pdb=" C05 G4C R 502 "
       pdb=" N04 G4C R 502 "
    ideal  model  delta    sigma   weight residual
    1.355  1.497 -0.142 2.00e-02 2.50e+03 5.03e+01
  bond pdb=" C03 G4C R 502 "
       pdb=" N04 G4C R 502 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" C   ILE R 205 "
       pdb=" N   PRO R 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.28e-02 6.10e+03 3.31e+00
  bond pdb=" C   MET R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.19e+00
  bond pdb=" C5  CLR R 505 "
       pdb=" C6  CLR R 505 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 2.00e-02 2.50e+03 2.53e+00
  ... (remaining 8697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 11335
        2.02 -     4.05: 409
        4.05 -     6.07: 34
        6.07 -     8.10: 13
        8.10 -    10.12: 4
  Bond angle restraints: 11795
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  130.97   -9.43 1.91e+00 2.74e-01 2.44e+01
  angle pdb=" C   ILE R 294 "
        pdb=" N   LEU R 295 "
        pdb=" CA  LEU R 295 "
      ideal   model   delta    sigma   weight residual
     121.62  127.01   -5.39 1.57e+00 4.06e-01 1.18e+01
  angle pdb=" CA  ASN B 119 "
        pdb=" CB  ASN B 119 "
        pdb=" CG  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     112.60  115.60   -3.00 1.00e+00 1.00e+00 8.97e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     122.40  126.70   -4.30 1.45e+00 4.76e-01 8.78e+00
  angle pdb=" N   MET R  78 "
        pdb=" CA  MET R  78 "
        pdb=" C   MET R  78 "
      ideal   model   delta    sigma   weight residual
     112.75  116.65   -3.90 1.36e+00 5.41e-01 8.23e+00
  ... (remaining 11790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5299
       17.89 -    35.77: 119
       35.77 -    53.65: 24
       53.65 -    71.54: 1
       71.54 -    89.42: 5
  Dihedral angle restraints: 5448
    sinusoidal: 2393
      harmonic: 3055
  Sorted by residual:
  dihedral pdb=" CB  CYS R 298 "
           pdb=" SG  CYS R 298 "
           pdb=" SG  CYS R 307 "
           pdb=" CB  CYS R 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.67  -87.33     1      1.00e+01 1.00e-02 9.15e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.82  -73.82     1      1.00e+01 1.00e-02 6.93e+01
  dihedral pdb=" CA  LEU B 198 "
           pdb=" C   LEU B 198 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.61   20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1173
       0.082 -    0.163: 126
       0.163 -    0.245: 19
       0.245 -    0.327: 6
       0.327 -    0.408: 5
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" C14 CLR R 507 "
            pdb=" C13 CLR R 507 "
            pdb=" C15 CLR R 507 "
            pdb=" C8  CLR R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" C14 CLR R 503 "
            pdb=" C13 CLR R 503 "
            pdb=" C15 CLR R 503 "
            pdb=" C8  CLR R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.39 2.00e-01 2.50e+01 3.73e+00
  ... (remaining 1326 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 G4C R 502 "   -0.215 2.00e-02 2.50e+03   1.50e-01 3.37e+02
        pdb=" C05 G4C R 502 "    0.047 2.00e-02 2.50e+03
        pdb=" C06 G4C R 502 "   -0.169 2.00e-02 2.50e+03
        pdb=" C16 G4C R 502 "    0.029 2.00e-02 2.50e+03
        pdb=" N04 G4C R 502 "    0.222 2.00e-02 2.50e+03
        pdb=" O15 G4C R 502 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 207 "    0.014 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   VAL R 207 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   VAL R 207 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R 208 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  93 "   -0.035 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO B  94 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  94 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  94 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 2234
        2.82 -     3.34: 7304
        3.34 -     3.86: 13145
        3.86 -     4.38: 15218
        4.38 -     4.90: 27054
  Nonbonded interactions: 64955
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OH  TYR A 170 "
            pdb=" OD2 ASP A 195 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER R 198 "
            pdb=" O2  LDP R 501 "
     model   vdw
     2.349 3.040
  ... (remaining 64950 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
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      :  0.004   0.142   8706  Z= 0.221
  Angle     :  0.853  10.120  11803  Z= 0.464
  Chirality :  0.062   0.408   1329
  Planarity :  0.007   0.150   1463
  Dihedral  :  8.668  89.425   3452
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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 are not related in a simple way.
  whole: -2.10 (0.23), residues: 1030
  helix: -1.11 (0.24), residues: 402
  sheet: -0.32 (0.34), residues: 218
  loop : -2.18 (0.25), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 150 
 TYR   0.014   0.002   TYR A 243 
 PHE   0.032   0.002   PHE A 108 
 TRP   0.028   0.002   TRP A 133 
 HIS   0.013   0.003   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8702)
  covalent geometry    : angle       0.85274 (11795)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       1.47153 (    8)
  hydrogen bonds       : bond        0.28320 (  427)
  hydrogen bonds       : angle       8.41991 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.319 
Fit side-chains
REVERT: R   35 LEU cc_start: 0.7128 (mt) cc_final: 0.6898 (mt)
REVERT: R   57 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7800 (mtmt)
REVERT: R  193 THR cc_start: 0.8282 (t) cc_final: 0.8063 (m)
REVERT: R  197 SER cc_start: 0.8489 (t) cc_final: 0.7878 (m)
REVERT: A  124 ASP cc_start: 0.7062 (m-30) cc_final: 0.6733 (m-30)
REVERT: A  237 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.7053 (mtt90)
REVERT: B   13 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7839 (pp30)
REVERT: B   66 ASP cc_start: 0.7119 (p0) cc_final: 0.6493 (t0)
REVERT: B  170 ASP cc_start: 0.8247 (t0) cc_final: 0.7930 (t0)
REVERT: B  178 THR cc_start: 0.7687 (m) cc_final: 0.7237 (p)
REVERT: G   21 MET cc_start: 0.7768 (mtt) cc_final: 0.7549 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1299
  time to fit residues: 34.8003
Evaluate side-chains
  138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
R  60 ASN
R 113 ASN
R 242 GLN
R 323 ASN
A  14 ASN
A  82 HIS
B  62 HIS
B  91 HIS
B 239 ASN
B 268 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.172337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.127526 restraints weight = 9052.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.92
r_work: 0.3226 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   8706  Z= 0.308
  Angle     :  0.738   8.199  11803  Z= 0.392
  Chirality :  0.049   0.183   1329
  Planarity :  0.005   0.051   1463
  Dihedral  :  6.988  84.973   1545
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  6.44 %
    Favored  : 91.68 %
  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 are not related in a simple way.
  whole: -0.65 (0.25), residues: 1030
  helix:  0.63 (0.24), residues: 413
  sheet: -0.29 (0.34), residues: 222
  loop : -1.60 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N 118 
 TYR   0.021   0.003   TYR N  94 
 PHE   0.033   0.003   PHE R 129 
 TRP   0.024   0.003   TRP B 169 
 HIS   0.011   0.003   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00725 ( 8702)
  covalent geometry    : angle       0.73700 (11795)
  SS BOND              : bond        0.00474 (    4)
  SS BOND              : angle       1.54308 (    8)
  hydrogen bonds       : bond        0.07889 (  427)
  hydrogen bonds       : angle       5.55923 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.240 
Fit side-chains
REVERT: R  283 CYS cc_start: 0.8065 (t) cc_final: 0.7644 (m)
REVERT: R  333 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6408 (m-10)
REVERT: A  163 TYR cc_start: 0.7651 (m-80) cc_final: 0.7388 (m-80)
REVERT: A  192 PHE cc_start: 0.8686 (t80) cc_final: 0.8420 (t80)
REVERT: B   13 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7768 (pp30)
REVERT: B   66 ASP cc_start: 0.7321 (p0) cc_final: 0.6948 (t0)
REVERT: B  197 ARG cc_start: 0.8606 (mmm160) cc_final: 0.8043 (mtp85)
REVERT: G   21 MET cc_start: 0.8348 (mtt) cc_final: 0.7597 (tmm)
REVERT: N   25 SER cc_start: 0.8421 (t) cc_final: 0.8019 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 159
  average time/residue: 0.0957
  time to fit residues: 20.9335
Evaluate side-chains
  132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 6 optimal weight:    0.2980
   chunk 94 optimal weight:    0.0060
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
R 242 GLN
R 323 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.181206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.136830 restraints weight = 8856.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.86
r_work: 0.3355 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8706  Z= 0.118
  Angle     :  0.510   6.525  11803  Z= 0.273
  Chirality :  0.041   0.141   1329
  Planarity :  0.004   0.046   1463
  Dihedral  :  6.297  80.821   1545
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  7.88 %
    Favored  : 90.01 %
  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 are not related in a simple way.
  whole:  0.48 (0.26), residues: 1030
  helix:  2.06 (0.25), residues: 402
  sheet: -0.17 (0.34), residues: 224
  loop : -1.21 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 226 
 TYR   0.021   0.001   TYR N  60 
 PHE   0.013   0.001   PHE R 141 
 TRP   0.020   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 8702)
  covalent geometry    : angle       0.50942 (11795)
  SS BOND              : bond        0.00065 (    4)
  SS BOND              : angle       0.82187 (    8)
  hydrogen bonds       : bond        0.05246 (  427)
  hydrogen bonds       : angle       4.71909 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.301 
Fit side-chains
REVERT: R  226 ARG cc_start: 0.7616 (mtt-85) cc_final: 0.7336 (mtt90)
REVERT: R  233 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6290 (mtp85)
REVERT: R  283 CYS cc_start: 0.7871 (t) cc_final: 0.7626 (m)
REVERT: A  233 ASP cc_start: 0.8308 (m-30) cc_final: 0.8076 (m-30)
REVERT: B   66 ASP cc_start: 0.7181 (p0) cc_final: 0.6752 (t0)
REVERT: B  195 ASP cc_start: 0.8381 (t0) cc_final: 0.8095 (t0)
REVERT: B  197 ARG cc_start: 0.8489 (mmm160) cc_final: 0.7975 (mtp85)
REVERT: G   21 MET cc_start: 0.8306 (mtt) cc_final: 0.7567 (tmm)
  outliers start: 19
  outliers final: 11
  residues processed: 144
  average time/residue: 0.1020
  time to fit residues: 20.0451
Evaluate side-chains
  115 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  269 LYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  132 LYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  109 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0970
   chunk 98 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 97 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.179747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.134143 restraints weight = 9061.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.19
r_work: 0.3299 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8706  Z= 0.122
  Angle     :  0.508   8.991  11803  Z= 0.268
  Chirality :  0.040   0.147   1329
  Planarity :  0.003   0.049   1463
  Dihedral  :  6.114  78.986   1545
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.21 %
    Favored  : 88.35 %
  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 are not related in a simple way.
  whole:  0.71 (0.26), residues: 1030
  helix:  2.35 (0.26), residues: 402
  sheet: -0.19 (0.34), residues: 223
  loop : -1.10 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 226 
 TYR   0.021   0.001   TYR A 163 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8702)
  covalent geometry    : angle       0.50575 (11795)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       1.77834 (    8)
  hydrogen bonds       : bond        0.04916 (  427)
  hydrogen bonds       : angle       4.56879 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.298 
Fit side-chains
REVERT: R  283 CYS cc_start: 0.8031 (t) cc_final: 0.7829 (m)
REVERT: A  233 ASP cc_start: 0.8421 (m-30) cc_final: 0.8214 (m-30)
REVERT: B   66 ASP cc_start: 0.7167 (p0) cc_final: 0.6740 (t0)
REVERT: G   21 MET cc_start: 0.8258 (mtt) cc_final: 0.7542 (tmm)
  outliers start: 22
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0897
  time to fit residues: 15.5902
Evaluate side-chains
  119 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  269 LYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  109 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0270
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6240

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.181071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.137591 restraints weight = 8954.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.94
r_work: 0.3317 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8706  Z= 0.108
  Angle     :  0.503  10.167  11803  Z= 0.260
  Chirality :  0.040   0.144   1329
  Planarity :  0.003   0.049   1463
  Dihedral  :  5.876  75.939   1545
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.77 %
    Favored  : 87.79 %
  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 are not related in a simple way.
  whole:  1.00 (0.26), residues: 1030
  helix:  2.71 (0.25), residues: 396
  sheet: -0.21 (0.33), residues: 229
  loop : -0.90 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 226 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.017   0.001   PHE A 192 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8702)
  covalent geometry    : angle       0.50163 (11795)
  SS BOND              : bond        0.00088 (    4)
  SS BOND              : angle       1.56703 (    8)
  hydrogen bonds       : bond        0.04473 (  427)
  hydrogen bonds       : angle       4.37404 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   85 GLU cc_start: 0.6676 (tp30) cc_final: 0.6195 (tp30)
REVERT: A   40 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7105 (m)
REVERT: B   66 ASP cc_start: 0.7093 (p0) cc_final: 0.6698 (t0)
REVERT: B  111 TYR cc_start: 0.8893 (m-80) cc_final: 0.8663 (m-80)
REVERT: G   21 MET cc_start: 0.8276 (mtt) cc_final: 0.7588 (tmm)
  outliers start: 22
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0964
  time to fit residues: 17.3499
Evaluate side-chains
  117 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 37 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.175661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.131180 restraints weight = 8829.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.95
r_work: 0.3255 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8706  Z= 0.148
  Angle     :  0.535   8.535  11803  Z= 0.280
  Chirality :  0.041   0.158   1329
  Planarity :  0.004   0.052   1463
  Dihedral  :  5.917  71.440   1545
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  :  9.32 %
    Favored  : 87.46 %
  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 are not related in a simple way.
  whole:  0.81 (0.26), residues: 1030
  helix:  2.42 (0.25), residues: 408
  sheet: -0.23 (0.33), residues: 228
  loop : -1.02 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 227 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.014   0.001   PHE A  81 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8702)
  covalent geometry    : angle       0.53365 (11795)
  SS BOND              : bond        0.00199 (    4)
  SS BOND              : angle       1.70204 (    8)
  hydrogen bonds       : bond        0.04874 (  427)
  hydrogen bonds       : angle       4.47890 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: R  163 TRP cc_start: 0.5321 (m100) cc_final: 0.4492 (t60)
REVERT: R  333 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7285 (m-10)
REVERT: A   40 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7582 (m)
REVERT: A   60 MET cc_start: 0.5149 (ttt) cc_final: 0.4901 (ttm)
REVERT: A   83 MET cc_start: 0.8592 (ttp) cc_final: 0.8299 (ttp)
REVERT: B   32 GLN cc_start: 0.7688 (tt0) cc_final: 0.7477 (tt0)
REVERT: B   66 ASP cc_start: 0.7143 (p0) cc_final: 0.6711 (t0)
REVERT: B  197 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8490 (mtp85)
REVERT: G   21 MET cc_start: 0.8194 (mtt) cc_final: 0.7633 (tmm)
  outliers start: 29
  outliers final: 23
  residues processed: 133
  average time/residue: 0.0903
  time to fit residues: 16.8505
Evaluate side-chains
  130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.1388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.176222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.130931 restraints weight = 8979.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.88
r_work: 0.3269 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8706  Z= 0.136
  Angle     :  0.526   8.611  11803  Z= 0.275
  Chirality :  0.041   0.172   1329
  Planarity :  0.003   0.053   1463
  Dihedral  :  5.777  68.538   1545
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.43 %
    Favored  : 86.68 %
  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 are not related in a simple way.
  whole:  0.93 (0.26), residues: 1030
  helix:  2.57 (0.25), residues: 402
  sheet: -0.28 (0.33), residues: 229
  loop : -0.88 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 237 
 TYR   0.021   0.001   TYR B 105 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8702)
  covalent geometry    : angle       0.52451 (11795)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       1.54355 (    8)
  hydrogen bonds       : bond        0.04698 (  427)
  hydrogen bonds       : angle       4.47019 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: R  163 TRP cc_start: 0.5304 (m100) cc_final: 0.4348 (t60)
REVERT: R  333 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7350 (m-10)
REVERT: A   40 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7668 (m)
REVERT: A   83 MET cc_start: 0.8555 (ttp) cc_final: 0.8320 (ttp)
REVERT: B   66 ASP cc_start: 0.6942 (p0) cc_final: 0.6629 (t0)
REVERT: G   21 MET cc_start: 0.8141 (mtt) cc_final: 0.7601 (tmm)
  outliers start: 26
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0957
  time to fit residues: 16.7369
Evaluate side-chains
  122 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0370
   chunk 38 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7860

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.177869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.132096 restraints weight = 8890.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.17
r_work: 0.3278 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8706  Z= 0.117
  Angle     :  0.508   8.576  11803  Z= 0.265
  Chirality :  0.040   0.165   1329
  Planarity :  0.003   0.054   1463
  Dihedral  :  5.449  65.339   1545
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.77 %
    Favored  : 86.57 %
  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 are not related in a simple way.
  whole:  1.06 (0.27), residues: 1030
  helix:  2.74 (0.25), residues: 397
  sheet: -0.27 (0.33), residues: 228
  loop : -0.80 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 226 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.021   0.001   PHE A 192 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8702)
  covalent geometry    : angle       0.50725 (11795)
  SS BOND              : bond        0.00059 (    4)
  SS BOND              : angle       1.42518 (    8)
  hydrogen bonds       : bond        0.04377 (  427)
  hydrogen bonds       : angle       4.35282 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  163 TRP cc_start: 0.5455 (m100) cc_final: 0.4458 (t60)
REVERT: A   25 MET cc_start: 0.6288 (mmp) cc_final: 0.6087 (mtp)
REVERT: A   40 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7559 (m)
REVERT: A   60 MET cc_start: 0.5277 (ttt) cc_final: 0.5070 (ttm)
REVERT: A   83 MET cc_start: 0.8516 (ttp) cc_final: 0.8276 (ttp)
REVERT: B   66 ASP cc_start: 0.6910 (p0) cc_final: 0.6628 (t0)
REVERT: G   21 MET cc_start: 0.8121 (mtt) cc_final: 0.7586 (tmm)
  outliers start: 24
  outliers final: 19
  residues processed: 130
  average time/residue: 0.0996
  time to fit residues: 17.8116
Evaluate side-chains
  129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    0.0030
   chunk 69 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0870
   chunk 20 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.4568

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

Flipped N/Q/H residues before XYZ refinement:
N  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.179255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.133633 restraints weight = 8924.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.99
r_work: 0.3316 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8706  Z= 0.104
  Angle     :  0.498   8.368  11803  Z= 0.259
  Chirality :  0.040   0.158   1329
  Planarity :  0.003   0.054   1463
  Dihedral  :  5.205  62.986   1545
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.43 %
    Favored  : 86.13 %
  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 are not related in a simple way.
  whole:  1.17 (0.27), residues: 1030
  helix:  2.87 (0.26), residues: 397
  sheet: -0.16 (0.33), residues: 228
  loop : -0.81 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 226 
 TYR   0.019   0.001   TYR N  60 
 PHE   0.022   0.001   PHE A 192 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 8702)
  covalent geometry    : angle       0.49732 (11795)
  SS BOND              : bond        0.00032 (    4)
  SS BOND              : angle       1.36416 (    8)
  hydrogen bonds       : bond        0.04088 (  427)
  hydrogen bonds       : angle       4.25939 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: R  163 TRP cc_start: 0.5453 (m100) cc_final: 0.4420 (t60)
REVERT: A   40 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (m)
REVERT: A   83 MET cc_start: 0.8443 (ttp) cc_final: 0.8184 (ttp)
REVERT: B   66 ASP cc_start: 0.6945 (p0) cc_final: 0.6609 (t0)
REVERT: G   21 MET cc_start: 0.8111 (mtt) cc_final: 0.7583 (tmm)
REVERT: N   35 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7663 (p0)
REVERT: N  110 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7199 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1020
  time to fit residues: 17.4625
Evaluate side-chains
  123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 76 optimal weight:    0.0980
   chunk 70 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0980
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.6184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.174454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129591 restraints weight = 8977.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.97
r_work: 0.3238 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8706  Z= 0.167
  Angle     :  0.556   8.182  11803  Z= 0.292
  Chirality :  0.042   0.173   1329
  Planarity :  0.004   0.053   1463
  Dihedral  :  5.380  59.334   1545
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.76 %
    Favored  : 85.79 %
  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 are not related in a simple way.
  whole:  0.95 (0.26), residues: 1030
  helix:  2.57 (0.25), residues: 403
  sheet: -0.28 (0.33), residues: 228
  loop : -0.84 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 237 
 TYR   0.018   0.002   TYR B 105 
 PHE   0.025   0.002   PHE A 192 
 TRP   0.024   0.002   TRP N  36 
 HIS   0.005   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8702)
  covalent geometry    : angle       0.55483 (11795)
  SS BOND              : bond        0.00216 (    4)
  SS BOND              : angle       1.46428 (    8)
  hydrogen bonds       : bond        0.04771 (  427)
  hydrogen bonds       : angle       4.55622 ( 1236)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: R  163 TRP cc_start: 0.5488 (m100) cc_final: 0.4583 (t60)
REVERT: A   40 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7831 (m)
REVERT: B   66 ASP cc_start: 0.6938 (p0) cc_final: 0.6645 (t0)
REVERT: B  188 MET cc_start: 0.8297 (mmm) cc_final: 0.8063 (mmm)
REVERT: G   21 MET cc_start: 0.8083 (mtt) cc_final: 0.7579 (tmm)
  outliers start: 22
  outliers final: 19
  residues processed: 120
  average time/residue: 0.0922
  time to fit residues: 15.5636
Evaluate side-chains
  123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  109 ASP
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.176439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.131412 restraints weight = 8868.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.91
r_work: 0.3281 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8706  Z= 0.121
  Angle     :  0.516   8.241  11803  Z= 0.271
  Chirality :  0.041   0.163   1329
  Planarity :  0.003   0.051   1463
  Dihedral  :  5.290  56.545   1545
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.65 %
    Favored  : 85.79 %
  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 are not related in a simple way.
  whole:  1.03 (0.27), residues: 1030
  helix:  2.71 (0.25), residues: 397
  sheet: -0.23 (0.33), residues: 226
  loop : -0.83 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 226 
 TYR   0.019   0.001   TYR N  60 
 PHE   0.024   0.001   PHE A 192 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8702)
  covalent geometry    : angle       0.51503 (11795)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       1.32456 (    8)
  hydrogen bonds       : bond        0.04394 (  427)
  hydrogen bonds       : angle       4.40828 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2847.55 seconds
wall clock time: 49 minutes 18.89 seconds (2958.89 seconds total)