Starting phenix.real_space_refine
on Wed Mar 12 07:41:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oy9_20222/03_2025/6oy9_20222.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.436
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    4810      2.51       5
     N    1249      2.21       5
     O    1397      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7519
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1809
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 494
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "R"
      Number of atoms: 2589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2589
          Classifications: {'peptide': 326}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 307}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 4.71, per 1000 atoms: 0.63
  Number of scatterers: 7519
  At special positions: 0
  Unit cell: (73.1, 124.7, 122.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1397      8.00
     N    1249      7.00
     C    4810      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 991.4 milliseconds
  

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 9 sheets defined
      40.0% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 27
    Processing helix  chain 'A' and resid 41 through 48
    Processing helix  chain 'A' and resid 203 through 212
      removed outlier: 3.691A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 203 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   TRP A 207 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   ILE A 208 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   HIS A 209 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 251
      removed outlier: 3.596A  pdb=" N   GLU A 241 " --> pdb=" O   ASN A 237 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS A 250 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ASN A 251 " --> pdb=" O   ASN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 291 through 305
      removed outlier: 3.556A  pdb=" N   ALA A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ASN A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 300 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 336
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.930A  pdb=" N   LEU A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS A 345 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP A 346 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 23
      removed outlier: 3.523A  pdb=" N   LEU B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.883A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 26
      removed outlier: 4.316A  pdb=" N   LEU G  15 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   LYS G  16 " --> pdb=" O   LYS G  12 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL G  26 " --> pdb=" O   LEU G  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 48
      removed outlier: 3.957A  pdb=" N   ARG G  47 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 51
      No H-bonds generated for 'chain 'G' and resid 49 through 51'
    Processing helix  chain 'R' and resid 33 through 65
      removed outlier: 3.561A  pdb=" N   PHE R  37 " --> pdb=" O   GLU R  33 " (cutoff:3.500A)
      Proline residue:  R  53  - end of helix
      removed outlier: 3.973A  pdb=" N   HIS R  65 " --> pdb=" O   VAL R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 89
      removed outlier: 3.687A  pdb=" N   ASP R  83 " --> pdb=" O   LEU R  79 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU R  84 " --> pdb=" O   ALA R  80 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET R  86 " --> pdb=" O   ALA R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 100
    Processing helix  chain 'R' and resid 106 through 141
      removed outlier: 4.139A  pdb=" N   PHE R 115 " --> pdb=" O   ASN R 111 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY R 120 " --> pdb=" O   PHE R 116 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLY R 121 " --> pdb=" O   ALA R 117 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS R 141 " --> pdb=" O   VAL R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 167
    Processing helix  chain 'R' and resid 195 through 198
      removed outlier: 3.666A  pdb=" N   THR R 198 " --> pdb=" O   HIS R 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 195 through 198'
    Processing helix  chain 'R' and resid 199 through 211
      removed outlier: 3.666A  pdb=" N   PHE R 203 " --> pdb=" O   ASN R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 235
    Processing helix  chain 'R' and resid 240 through 266
      removed outlier: 3.724A  pdb=" N   GLN R 244 " --> pdb=" O   SER R 240 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   LYS R 248 " --> pdb=" O   GLN R 244 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ILE R 255 " --> pdb=" O   THR R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 266 through 278
    Processing helix  chain 'R' and resid 286 through 288
      No H-bonds generated for 'chain 'R' and resid 286 through 288'
    Processing helix  chain 'R' and resid 289 through 297
    Processing helix  chain 'R' and resid 298 through 300
      No H-bonds generated for 'chain 'R' and resid 298 through 300'
    Processing helix  chain 'R' and resid 313 through 318
    Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 195
      removed outlier: 3.570A  pdb=" N   ARG A 193 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A  34 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE A 218 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU A  33 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ILE A 217 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 4.110A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY B 319 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.154A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   MET B  61 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   LEU B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE B  81 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 104
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.878A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.989A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.611A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.372A  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: 7.117A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 4 through 5

    286 hydrogen bonds defined for protein.
    825 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: 1.75

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2300
        1.34 -     1.45: 1462
        1.45 -     1.57: 3827
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 7683
  Sorted by residual:
  bond pdb=" C7  RET R 401 "
       pdb=" C8  RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.298  0.051 2.00e-02 2.50e+03 6.44e+00
  bond pdb=" CA  LEU B 336 "
       pdb=" CB  LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.525  1.492  0.033 1.47e-02 4.63e+03 5.06e+00
  bond pdb=" CB  PHE B 234 "
       pdb=" CG  PHE B 234 "
    ideal  model  delta    sigma   weight residual
    1.502  1.451  0.051 2.30e-02 1.89e+03 4.95e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.431  0.067 3.10e-02 1.04e+03 4.61e+00
  bond pdb=" C   PHE B 199 "
       pdb=" N   VAL B 200 "
    ideal  model  delta    sigma   weight residual
    1.327  1.269  0.058 2.97e-02 1.13e+03 3.84e+00
  ... (remaining 7678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 10216
        3.49 -     6.98: 159
        6.98 -    10.47: 16
       10.47 -    13.96: 3
       13.96 -    17.45: 1
  Bond angle restraints: 10395
  Sorted by residual:
  angle pdb=" CA  LEU G  32 "
        pdb=" CB  LEU G  32 "
        pdb=" CG  LEU G  32 "
      ideal   model   delta    sigma   weight residual
     116.30  133.75  -17.45 3.50e+00 8.16e-02 2.48e+01
  angle pdb=" C   VAL R 300 "
        pdb=" N   TYR R 301 "
        pdb=" CA  TYR R 301 "
      ideal   model   delta    sigma   weight residual
     122.38  114.17    8.21 1.81e+00 3.05e-01 2.06e+01
  angle pdb=" C   GLU R  25 "
        pdb=" N   ALA R  26 "
        pdb=" CA  ALA R  26 "
      ideal   model   delta    sigma   weight residual
     121.80  132.53  -10.73 2.44e+00 1.68e-01 1.93e+01
  angle pdb=" CA  PRO R 291 "
        pdb=" N   PRO R 291 "
        pdb=" CD  PRO R 291 "
      ideal   model   delta    sigma   weight residual
     112.00  106.52    5.48 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" C   CYS R 322 "
        pdb=" N   CYS R 323 "
        pdb=" CA  CYS R 323 "
      ideal   model   delta    sigma   weight residual
     122.08  127.41   -5.33 1.47e+00 4.63e-01 1.31e+01
  ... (remaining 10390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 3915
       16.99 -    33.98: 526
       33.98 -    50.98: 95
       50.98 -    67.97: 13
       67.97 -    84.96: 5
  Dihedral angle restraints: 4554
    sinusoidal: 1805
      harmonic: 2749
  Sorted by residual:
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.86   53.86     1      1.00e+01 1.00e-02 3.94e+01
  dihedral pdb=" CA  LYS A 275 "
           pdb=" C   LYS A 275 "
           pdb=" N   LYS A 276 "
           pdb=" CA  LYS A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.10  -26.90     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  ASP B 118 "
           pdb=" C   ASP B 118 "
           pdb=" N   ASN B 119 "
           pdb=" CA  ASN B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.61  -25.39     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 4551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1050
       0.112 -    0.224: 105
       0.224 -    0.336: 1
       0.336 -    0.448: 0
       0.448 -    0.561: 1
  Chirality restraints: 1157
  Sorted by residual:
  chirality pdb=" CB  ILE R 214 "
            pdb=" CA  ILE R 214 "
            pdb=" CG1 ILE R 214 "
            pdb=" CG2 ILE R 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.08    0.56 2.00e-01 2.50e+01 7.86e+00
  chirality pdb=" CB  VAL B 320 "
            pdb=" CA  VAL B 320 "
            pdb=" CG1 VAL B 320 "
            pdb=" CG2 VAL B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  ILE B  43 "
            pdb=" CA  ILE B  43 "
            pdb=" CG1 ILE B  43 "
            pdb=" CG2 ILE B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1154 not shown)

  Planarity restraints: 1326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  70 "    0.072 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO R  71 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO R  71 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R  71 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 170 "    0.068 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO R 171 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO R 171 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO R 171 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "    0.021 2.00e-02 2.50e+03   2.05e-02 1.06e+01
        pdb=" CG  TRP B  82 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1323 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2147
        2.80 -     3.32: 6890
        3.32 -     3.85: 11894
        3.85 -     4.37: 12456
        4.37 -     4.90: 21424
  Nonbonded interactions: 54811
  Sorted by model distance:
  nonbonded pdb=" O   SER B  84 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER R  22 "
            pdb=" OE1 GLU R  25 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   SER R 298 "
            pdb=" OG  SER R 298 "
     model   vdw
     2.304 3.040
  ... (remaining 54806 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.510
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
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      :  0.009   0.089   7683  Z= 0.603
  Angle     :  1.097  17.446  10395  Z= 0.589
  Chirality :  0.065   0.561   1157
  Planarity :  0.008   0.108   1326
  Dihedral  : 15.304  84.962   2777
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 17.56 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.69 (0.21), residues: 938
  helix: -2.38 (0.22), residues: 348
  sheet: -3.07 (0.36), residues: 135
  loop : -3.78 (0.21), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.004   TRP B  82 
 HIS   0.009   0.002   HIS B  54 
 PHE   0.022   0.003   PHE B 241 
 TYR   0.038   0.004   TYR R  96 
 ARG   0.005   0.000   ARG G  30 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8397 (ptp90)
REVERT: A   49 MET cc_start: 0.8944 (tpp) cc_final: 0.8415 (mmm)
REVERT: A  193 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8649 (mtp85)
REVERT: A  238 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8474 (ttp-170)
REVERT: A  306 LEU cc_start: 0.9248 (tp) cc_final: 0.8920 (tp)
REVERT: B  215 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: B  260 GLU cc_start: 0.8122 (mp0) cc_final: 0.7888 (mp0)
REVERT: B  271 CYS cc_start: 0.7359 (p) cc_final: 0.6616 (p)
REVERT: B  290 ASP cc_start: 0.7761 (m-30) cc_final: 0.7186 (m-30)
REVERT: B  325 MET cc_start: 0.8172 (mmt) cc_final: 0.7877 (mmm)
REVERT: G   12 LYS cc_start: 0.7789 (mttt) cc_final: 0.7407 (mmmt)
REVERT: R   44 MET cc_start: 0.8920 (tpp) cc_final: 0.8666 (tpp)
REVERT: R   69 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7844 (ttm-80)
REVERT: R  179 ILE cc_start: 0.8710 (mt) cc_final: 0.8494 (tp)
REVERT: R  190 ASP cc_start: 0.7536 (p0) cc_final: 0.7011 (p0)
REVERT: R  200 ASN cc_start: 0.7987 (t0) cc_final: 0.6630 (t0)
REVERT: R  231 LYS cc_start: 0.8897 (tppt) cc_final: 0.8596 (tmtt)
  outliers start: 2
  outliers final: 2
  residues processed: 154
  average time/residue: 0.2311
  time to fit residues: 45.9095
Evaluate side-chains
  116 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  176 SER
Chi-restraints excluded: chain R residue  198 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B  16 ASN
B 156 GLN
B 183 HIS
B 293 ASN
B 311 HIS
R 100 HIS
R 238 GLN
R 278 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.094234 restraints weight = 15115.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097017 restraints weight = 8635.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.098864 restraints weight = 6047.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7683  Z= 0.258
  Angle     :  0.708  15.384  10395  Z= 0.368
  Chirality :  0.044   0.254   1157
  Planarity :  0.006   0.083   1326
  Dihedral  :  6.245  42.085   1027
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.22 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.25), residues: 938
  helix: -0.55 (0.27), residues: 353
  sheet: -2.53 (0.40), residues: 137
  loop : -3.37 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R  35 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.025   0.002   PHE B 235 
 TYR   0.030   0.002   TYR R  96 
 ARG   0.002   0.000   ARG A 201 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8623 (ptp-170) cc_final: 0.8377 (ptp90)
REVERT: A   49 MET cc_start: 0.8925 (tpp) cc_final: 0.8297 (mmm)
REVERT: A  238 ARG cc_start: 0.8641 (ttm170) cc_final: 0.8109 (mmp-170)
REVERT: A  243 MET cc_start: 0.9065 (mmm) cc_final: 0.8842 (mmm)
REVERT: A  306 LEU cc_start: 0.9152 (tp) cc_final: 0.8496 (tt)
REVERT: B  215 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: B  262 MET cc_start: 0.8433 (tpt) cc_final: 0.8065 (tpp)
REVERT: B  271 CYS cc_start: 0.6958 (p) cc_final: 0.6240 (p)
REVERT: B  290 ASP cc_start: 0.7662 (m-30) cc_final: 0.7032 (m-30)
REVERT: B  317 CYS cc_start: 0.8462 (t) cc_final: 0.8255 (t)
REVERT: G   12 LYS cc_start: 0.7637 (mttt) cc_final: 0.7259 (mmmt)
REVERT: R   44 MET cc_start: 0.8898 (tpp) cc_final: 0.8674 (tpp)
REVERT: R   69 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7805 (ttm-80)
REVERT: R  176 SER cc_start: 0.9216 (p) cc_final: 0.8830 (m)
REVERT: R  179 ILE cc_start: 0.8844 (mt) cc_final: 0.8560 (tp)
REVERT: R  183 MET cc_start: 0.8549 (mtt) cc_final: 0.8326 (mmp)
REVERT: R  190 ASP cc_start: 0.7836 (p0) cc_final: 0.7191 (p0)
REVERT: R  200 ASN cc_start: 0.7550 (t0) cc_final: 0.6581 (t0)
  outliers start: 23
  outliers final: 9
  residues processed: 158
  average time/residue: 0.2152
  time to fit residues: 44.4961
Evaluate side-chains
  131 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  290 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 340 ASN
** G  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.111627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.087471 restraints weight = 15742.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.090146 restraints weight = 8952.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.091966 restraints weight = 6219.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7683  Z= 0.286
  Angle     :  0.703  13.310  10395  Z= 0.364
  Chirality :  0.044   0.273   1157
  Planarity :  0.005   0.074   1326
  Dihedral  :  5.822  37.430   1025
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.63 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.26), residues: 938
  helix:  0.25 (0.28), residues: 353
  sheet: -2.28 (0.43), residues: 135
  loop : -3.21 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R  35 
 HIS   0.010   0.001   HIS B 183 
 PHE   0.023   0.002   PHE B 235 
 TYR   0.026   0.002   TYR R  96 
 ARG   0.005   0.000   ARG B  96 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8274 (ptp90)
REVERT: A   49 MET cc_start: 0.8942 (tpp) cc_final: 0.8217 (mmm)
REVERT: A  238 ARG cc_start: 0.8621 (ttm170) cc_final: 0.8264 (ttp-170)
REVERT: A  243 MET cc_start: 0.9068 (mmm) cc_final: 0.8816 (mmm)
REVERT: A  306 LEU cc_start: 0.9169 (tp) cc_final: 0.8536 (tt)
REVERT: A  342 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: B  215 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: B  260 GLU cc_start: 0.8004 (mp0) cc_final: 0.7753 (mp0)
REVERT: B  262 MET cc_start: 0.8482 (tpt) cc_final: 0.7943 (tpp)
REVERT: G   12 LYS cc_start: 0.7635 (mttt) cc_final: 0.7273 (mmmt)
REVERT: R   44 MET cc_start: 0.8917 (tpp) cc_final: 0.8701 (tpp)
REVERT: R   69 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7715 (ttm-80)
REVERT: R  122 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8444 (tp30)
REVERT: R  176 SER cc_start: 0.9209 (p) cc_final: 0.8796 (m)
REVERT: R  179 ILE cc_start: 0.8837 (mt) cc_final: 0.8585 (tp)
REVERT: R  190 ASP cc_start: 0.7925 (p0) cc_final: 0.7356 (p0)
REVERT: R  200 ASN cc_start: 0.7919 (t0) cc_final: 0.6983 (t0)
REVERT: R  231 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8694 (ttmm)
  outliers start: 29
  outliers final: 16
  residues processed: 151
  average time/residue: 0.2015
  time to fit residues: 40.7416
Evaluate side-chains
  141 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  122 GLU
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:   50.0000
   chunk 53 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.3980
   chunk 88 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
R  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.123551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098461 restraints weight = 15084.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101371 restraints weight = 8503.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103316 restraints weight = 5918.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7683  Z= 0.148
  Angle     :  0.633  12.360  10395  Z= 0.317
  Chirality :  0.042   0.267   1157
  Planarity :  0.005   0.074   1326
  Dihedral  :  5.168  35.304   1025
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 26.34 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.27), residues: 938
  helix:  0.75 (0.29), residues: 354
  sheet: -1.94 (0.46), residues: 128
  loop : -3.09 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.016   0.001   PHE A 283 
 TYR   0.022   0.001   TYR R  96 
 ARG   0.003   0.000   ARG A 204 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7651 (mttt) cc_final: 0.6787 (tmtt)
REVERT: A  238 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8037 (mmp-170)
REVERT: A  306 LEU cc_start: 0.9156 (tp) cc_final: 0.8555 (tt)
REVERT: A  342 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: B  260 GLU cc_start: 0.8069 (mp0) cc_final: 0.7860 (mp0)
REVERT: B  262 MET cc_start: 0.8462 (tpt) cc_final: 0.7993 (tpt)
REVERT: B  271 CYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6051 (p)
REVERT: B  278 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7248 (m-10)
REVERT: G   12 LYS cc_start: 0.7525 (mttt) cc_final: 0.7201 (mmmt)
REVERT: G   20 ASP cc_start: 0.8176 (m-30) cc_final: 0.7429 (p0)
REVERT: R   44 MET cc_start: 0.8857 (tpp) cc_final: 0.8646 (tpp)
REVERT: R   69 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7629 (ttm-80)
REVERT: R  190 ASP cc_start: 0.7863 (p0) cc_final: 0.7242 (p0)
REVERT: R  200 ASN cc_start: 0.7443 (t0) cc_final: 0.6851 (t0)
REVERT: R  201 GLU cc_start: 0.7608 (tp30) cc_final: 0.7257 (tp30)
REVERT: R  231 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8657 (ttmm)
  outliers start: 28
  outliers final: 13
  residues processed: 173
  average time/residue: 0.1992
  time to fit residues: 45.8877
Evaluate side-chains
  148 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0670
   chunk 55 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.3924

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

Flipped N/Q/H residues before XYZ refinement:
G  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.121607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.096162 restraints weight = 15122.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099036 restraints weight = 8601.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.100959 restraints weight = 5995.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7683  Z= 0.209
  Angle     :  0.658  12.934  10395  Z= 0.330
  Chirality :  0.043   0.260   1157
  Planarity :  0.004   0.071   1326
  Dihedral  :  5.149  32.755   1025
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.71 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.28), residues: 938
  helix:  0.99 (0.29), residues: 354
  sheet: -1.87 (0.45), residues: 132
  loop : -3.00 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.016   0.001   PHE B 235 
 TYR   0.018   0.002   TYR R  96 
 ARG   0.004   0.000   ARG A 193 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7688 (mttt) cc_final: 0.6815 (tmtt)
REVERT: A  238 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8196 (ttp-170)
REVERT: A  306 LEU cc_start: 0.9115 (tp) cc_final: 0.8500 (tt)
REVERT: A  342 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7890 (tm-30)
REVERT: B  215 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7918 (mm-30)
REVERT: B  262 MET cc_start: 0.8415 (tpt) cc_final: 0.7886 (tpp)
REVERT: B  278 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7511 (m-10)
REVERT: R   44 MET cc_start: 0.8927 (tpp) cc_final: 0.8693 (tpp)
REVERT: R   69 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7599 (ttm-80)
REVERT: R   76 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8459 (tt)
REVERT: R  190 ASP cc_start: 0.7533 (p0) cc_final: 0.7297 (p0)
REVERT: R  200 ASN cc_start: 0.7789 (t0) cc_final: 0.6836 (t0)
REVERT: R  201 GLU cc_start: 0.7718 (tp30) cc_final: 0.7362 (tp30)
REVERT: R  231 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8671 (ttmm)
REVERT: R  311 LYS cc_start: 0.9047 (tppp) cc_final: 0.8785 (tppp)
  outliers start: 32
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1926
  time to fit residues: 43.3635
Evaluate side-chains
  155 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   21 GLN
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0060
   chunk 20 optimal weight:    4.9990
   chunk 25 optimal weight:   40.0000
   chunk 63 optimal weight:    6.9990
   overall best weight:    3.2004

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  21 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.120418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.094966 restraints weight = 15240.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.097782 restraints weight = 8690.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.099705 restraints weight = 6086.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7683  Z= 0.254
  Angle     :  0.693  15.621  10395  Z= 0.345
  Chirality :  0.044   0.270   1157
  Planarity :  0.004   0.070   1326
  Dihedral  :  5.193  33.711   1025
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 27.44 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.28), residues: 938
  helix:  1.09 (0.29), residues: 347
  sheet: -1.64 (0.48), residues: 124
  loop : -2.91 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R  35 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.021   0.001   PHE B 199 
 TYR   0.024   0.002   TYR B 111 
 ARG   0.004   0.000   ARG A 193 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7751 (mttt) cc_final: 0.6869 (tmtt)
REVERT: A  228 MET cc_start: 0.7960 (tpt) cc_final: 0.6951 (tpt)
REVERT: A  342 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: B  262 MET cc_start: 0.8431 (tpt) cc_final: 0.7815 (tpp)
REVERT: B  278 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7548 (m-10)
REVERT: B  325 MET cc_start: 0.8138 (mmt) cc_final: 0.7645 (tpp)
REVERT: G   12 LYS cc_start: 0.7454 (mmtp) cc_final: 0.7057 (mmmt)
REVERT: G   20 ASP cc_start: 0.8225 (m-30) cc_final: 0.7436 (p0)
REVERT: G   36 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7338 (p)
REVERT: R   44 MET cc_start: 0.8917 (tpp) cc_final: 0.8686 (tpp)
REVERT: R   76 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8540 (tt)
REVERT: R  190 ASP cc_start: 0.7195 (p0) cc_final: 0.6876 (p0)
REVERT: R  200 ASN cc_start: 0.7957 (t0) cc_final: 0.6788 (t0)
REVERT: R  201 GLU cc_start: 0.7727 (tp30) cc_final: 0.7337 (tp30)
REVERT: R  231 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8695 (ttmm)
  outliers start: 34
  outliers final: 26
  residues processed: 163
  average time/residue: 0.1933
  time to fit residues: 42.4909
Evaluate side-chains
  158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   22 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 25 optimal weight:   40.0000
   chunk 75 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 209 HIS
** G  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.117764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.092567 restraints weight = 15115.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.095216 restraints weight = 8959.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.096972 restraints weight = 6394.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7683  Z= 0.350
  Angle     :  0.748  14.853  10395  Z= 0.377
  Chirality :  0.045   0.274   1157
  Planarity :  0.005   0.069   1326
  Dihedral  :  5.409  34.115   1025
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.17 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.28), residues: 938
  helix:  0.95 (0.29), residues: 347
  sheet: -1.80 (0.46), residues: 130
  loop : -2.94 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R  35 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.018   0.002   PHE B 235 
 TYR   0.023   0.002   TYR B 111 
 ARG   0.008   0.000   ARG A 238 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 ARG cc_start: 0.8722 (ttm170) cc_final: 0.7755 (mmm-85)
REVERT: A  342 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8035 (tm-30)
REVERT: B  153 ASP cc_start: 0.8252 (p0) cc_final: 0.7913 (p0)
REVERT: B  262 MET cc_start: 0.8419 (tpt) cc_final: 0.8092 (tpp)
REVERT: B  278 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7487 (m-10)
REVERT: B  325 MET cc_start: 0.8162 (mmt) cc_final: 0.7767 (tpp)
REVERT: G   36 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7325 (p)
REVERT: R   44 MET cc_start: 0.8924 (tpp) cc_final: 0.8711 (tpp)
REVERT: R   76 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8607 (tt)
REVERT: R  200 ASN cc_start: 0.8111 (t0) cc_final: 0.7145 (t0)
REVERT: R  201 GLU cc_start: 0.7820 (tp30) cc_final: 0.7451 (tp30)
REVERT: R  231 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8656 (ttmm)
  outliers start: 40
  outliers final: 29
  residues processed: 163
  average time/residue: 0.1959
  time to fit residues: 42.9876
Evaluate side-chains
  157 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  309 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   chunk 91 optimal weight:    0.4980
   chunk 67 optimal weight:    9.9990
   chunk 75 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.122094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.096942 restraints weight = 15103.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099756 restraints weight = 8791.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.101497 restraints weight = 6188.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7683  Z= 0.195
  Angle     :  0.700  14.796  10395  Z= 0.346
  Chirality :  0.043   0.243   1157
  Planarity :  0.004   0.071   1326
  Dihedral  :  5.071  32.602   1025
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 30.12 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.28), residues: 938
  helix:  1.14 (0.30), residues: 347
  sheet: -1.58 (0.48), residues: 125
  loop : -2.88 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  35 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.021   0.001   PHE B 235 
 TYR   0.023   0.002   TYR B 111 
 ARG   0.004   0.000   ARG A 193 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7666 (mttt) cc_final: 0.6762 (tmtt)
REVERT: A  342 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: B  170 ASP cc_start: 0.7550 (t0) cc_final: 0.7264 (t0)
REVERT: B  262 MET cc_start: 0.8413 (tpt) cc_final: 0.7952 (tpp)
REVERT: B  278 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7562 (m-10)
REVERT: B  325 MET cc_start: 0.8068 (mmt) cc_final: 0.7661 (tpp)
REVERT: G   12 LYS cc_start: 0.7322 (mmtp) cc_final: 0.6925 (mmmt)
REVERT: G   20 ASP cc_start: 0.8177 (m-30) cc_final: 0.7411 (p0)
REVERT: G   36 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7326 (p)
REVERT: R   44 MET cc_start: 0.8903 (tpp) cc_final: 0.8678 (tpp)
REVERT: R   76 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8529 (tt)
REVERT: R  190 ASP cc_start: 0.7262 (p0) cc_final: 0.6980 (p0)
REVERT: R  200 ASN cc_start: 0.7996 (t0) cc_final: 0.7706 (t0)
REVERT: R  201 GLU cc_start: 0.7614 (tp30) cc_final: 0.7184 (tp30)
REVERT: R  231 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8670 (ttmm)
  outliers start: 28
  outliers final: 22
  residues processed: 158
  average time/residue: 0.1917
  time to fit residues: 40.7026
Evaluate side-chains
  158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  309 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 92 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 83 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.9060

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.126742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.100760 restraints weight = 15039.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.103759 restraints weight = 8353.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.105730 restraints weight = 5762.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7683  Z= 0.169
  Angle     :  0.692  14.664  10395  Z= 0.338
  Chirality :  0.042   0.242   1157
  Planarity :  0.004   0.072   1326
  Dihedral  :  4.784  32.760   1025
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 30.49 %
    Favored  : 66.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.28), residues: 938
  helix:  1.31 (0.30), residues: 346
  sheet: -1.35 (0.48), residues: 125
  loop : -2.77 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 297 
 HIS   0.002   0.000   HIS B 311 
 PHE   0.021   0.001   PHE B 199 
 TYR   0.023   0.001   TYR A 286 
 ARG   0.005   0.000   ARG A 193 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7686 (mttt) cc_final: 0.6818 (tmtt)
REVERT: A  238 ARG cc_start: 0.8597 (ttm170) cc_final: 0.7608 (mmm-85)
REVERT: A  342 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: B  153 ASP cc_start: 0.8025 (p0) cc_final: 0.7701 (p0)
REVERT: B  217 MET cc_start: 0.8429 (mtm) cc_final: 0.8094 (mtp)
REVERT: B  221 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7572 (p)
REVERT: B  262 MET cc_start: 0.8306 (tpt) cc_final: 0.7763 (tpp)
REVERT: B  264 TYR cc_start: 0.8046 (m-80) cc_final: 0.7618 (m-80)
REVERT: B  278 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7656 (m-10)
REVERT: B  325 MET cc_start: 0.8072 (mmt) cc_final: 0.7475 (tpp)
REVERT: G   12 LYS cc_start: 0.7265 (mmtp) cc_final: 0.7053 (mmmt)
REVERT: G   20 ASP cc_start: 0.8166 (m-30) cc_final: 0.7451 (p0)
REVERT: G   36 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (p)
REVERT: R   44 MET cc_start: 0.8847 (tpp) cc_final: 0.8634 (tpp)
REVERT: R   76 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (tt)
REVERT: R  190 ASP cc_start: 0.7288 (p0) cc_final: 0.6946 (p0)
REVERT: R  200 ASN cc_start: 0.7811 (t0) cc_final: 0.7449 (t0)
REVERT: R  201 GLU cc_start: 0.7506 (tp30) cc_final: 0.7083 (tp30)
REVERT: R  231 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8657 (ttmm)
  outliers start: 27
  outliers final: 20
  residues processed: 164
  average time/residue: 0.1936
  time to fit residues: 42.8509
Evaluate side-chains
  160 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  309 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 63 optimal weight:    0.4980
   chunk 2 optimal weight:    7.9990
   chunk 43 optimal weight:    0.4980
   chunk 40 optimal weight:    8.9990
   overall best weight:    3.3986

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** 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 = 0.3654 r_free = 0.3654 target = 0.120903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.095679 restraints weight = 15209.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098482 restraints weight = 8584.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100367 restraints weight = 6004.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7683  Z= 0.277
  Angle     :  0.738  14.331  10395  Z= 0.365
  Chirality :  0.044   0.265   1157
  Planarity :  0.004   0.070   1326
  Dihedral  :  5.025  31.921   1025
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 31.22 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.28), residues: 938
  helix:  1.15 (0.29), residues: 347
  sheet: -1.39 (0.48), residues: 127
  loop : -2.80 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.020   0.002   PHE B 235 
 TYR   0.023   0.002   TYR B 111 
 ARG   0.002   0.000   ARG A 238 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7700 (mttt) cc_final: 0.6820 (tmtt)
REVERT: A  238 ARG cc_start: 0.8687 (ttm170) cc_final: 0.7807 (mmp-170)
REVERT: A  342 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B  153 ASP cc_start: 0.8201 (p0) cc_final: 0.7840 (p0)
REVERT: B  262 MET cc_start: 0.8336 (tpt) cc_final: 0.7952 (tpp)
REVERT: B  278 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7584 (m-10)
REVERT: B  325 MET cc_start: 0.8188 (mmt) cc_final: 0.7620 (tpp)
REVERT: G   36 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7285 (p)
REVERT: R   44 MET cc_start: 0.8904 (tpp) cc_final: 0.8668 (tpp)
REVERT: R   76 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: R  190 ASP cc_start: 0.7422 (p0) cc_final: 0.7083 (p0)
REVERT: R  200 ASN cc_start: 0.8083 (t0) cc_final: 0.7704 (t0)
REVERT: R  201 GLU cc_start: 0.7724 (tp30) cc_final: 0.7244 (tp30)
REVERT: R  231 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8685 (ttmm)
REVERT: R  253 MET cc_start: 0.8782 (tpp) cc_final: 0.8547 (tpp)
  outliers start: 28
  outliers final: 22
  residues processed: 156
  average time/residue: 0.2092
  time to fit residues: 43.2676
Evaluate side-chains
  158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   85 PHE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  138 VAL
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  304 VAL
Chi-restraints excluded: chain R residue  309 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0170
   chunk 1 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.1224

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.127081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101131 restraints weight = 14855.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.104152 restraints weight = 8261.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.106085 restraints weight = 5710.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7683  Z= 0.178
  Angle     :  0.693  14.583  10395  Z= 0.339
  Chirality :  0.042   0.239   1157
  Planarity :  0.004   0.072   1326
  Dihedral  :  4.785  33.514   1025
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 31.95 %
    Favored  : 65.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.28), residues: 938
  helix:  1.27 (0.30), residues: 347
  sheet: -1.33 (0.46), residues: 136
  loop : -2.69 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 311 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.025   0.002   TYR A 286 
 ARG   0.003   0.000   ARG A 193 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2304.05 seconds
wall clock time: 40 minutes 51.64 seconds (2451.64 seconds total)