Starting phenix.real_space_refine
on Thu Jul  2 16:03:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vb1_64912/07_2026/9vb1_64912.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.008 sd=   0.076
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    5793      2.51       5
     N    1551      2.21       5
     O    1697      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9104
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1757
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 413
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "D"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2504
          Classifications: {'peptide': 316}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 53
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
  Time building chain proxies: 1.90, per 1000 atoms: 0.21
  Number of scatterers: 9104
  At special positions: 0
  Unit cell: (94.0667, 121.733, 124.5, 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    1697      8.00
     N    1551      7.00
     C    5793      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.07
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 153 " - pdb=" SG  CYS R 236 " distance=2.00
    Simple disulfide: pdb=" SG  CYS R 393 " - pdb=" SG  CYS R 395 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 462.6 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2180

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 16 sheets defined
      40.2% alpha, 25.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.274A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.287A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.854A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 22 through 44
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'C' and resid 9 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 87 through 91
    Processing helix  chain 'D' and resid 220 through 224
    Processing helix  chain 'R' and resid 71 through 103
      removed outlier: 3.502A  pdb=" N   LYS R  75 " --> pdb=" O   ASP R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 139
      removed outlier: 3.961A  pdb=" N   SER R 111 " --> pdb=" O   GLN R 107 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL R 113 " --> pdb=" O   LEU R 109 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   HIS R 114 " --> pdb=" O   GLN R 110 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   MET R 132 " --> pdb=" O   LEU R 128 " (cutoff:3.500A)
      Proline residue:  R 133  - end of helix
    Processing helix  chain 'R' and resid 148 through 184
    Processing helix  chain 'R' and resid 184 through 192
    Processing helix  chain 'R' and resid 193 through 212
    Processing helix  chain 'R' and resid 214 through 218
    Processing helix  chain 'R' and resid 241 through 257
    Processing helix  chain 'R' and resid 257 through 285
    Processing helix  chain 'R' and resid 305 through 341
      Proline residue:  R 330  - end of helix
    Processing helix  chain 'R' and resid 347 through 377
      removed outlier: 3.682A  pdb=" N   MET R 359 " --> pdb=" O   HIS R 355 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER R 369 " --> pdb=" O   PHE R 365 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN R 372 " --> pdb=" O   SER R 368 " (cutoff:3.500A)
      Proline residue:  R 373  - end of helix
    Processing helix  chain 'R' and resid 380 through 394
      removed outlier: 3.604A  pdb=" N   HIS R 385 " --> pdb=" O   ALA R 381 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ILE R 386 " --> pdb=" O   ASN R 382 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 191
      removed outlier: 7.004A  pdb=" N   GLY A 183 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   GLY A 202 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.326A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   GLY A 203 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 69
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81
      removed outlier: 3.523A  pdb=" N   ALA B  78 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LYS B  96 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ASP B 101 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   LYS B 107 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 123
      removed outlier: 6.700A  pdb=" N   GLY B 133 " --> pdb=" O   MET B 119 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   CYS B 121 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ALA B 131 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TYR B 123 " --> pdb=" O   TYR B 129 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   TYR B 129 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLY B 134 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ILE B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   CYS B 139 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLU B 156 " --> pdb=" O   CYS B 139 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE B 141 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG B 152 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 169
      removed outlier: 3.503A  pdb=" N   CYS B 166 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASP B 188 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   GLN B 194 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 210
      removed outlier: 6.744A  pdb=" N   GLY B 220 " --> pdb=" O   MET B 206 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LEU B 208 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL B 218 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   LEU B 210 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU B 216 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN B 238 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ASP B 230 " --> pdb=" O   CYS B 236 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   CYS B 236 " --> pdb=" O   ASP B 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 247 through 252
      removed outlier: 3.546A  pdb=" N   MET B 280 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ASP B 272 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   GLU B 278 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 296
      removed outlier: 3.647A  pdb=" N   SER B 293 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASN B 311 " --> pdb=" O   TYR B 307 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   ASP B 316 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ARG B 322 " --> pdb=" O   ASP B 316 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 333 through 337
      removed outlier: 3.523A  pdb=" N   CYS B 335 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.085A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.085A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 148
      removed outlier: 6.474A  pdb=" N   LEU D 174 " --> pdb=" O   TYR D 190 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR D 190 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   TRP D 176 " --> pdb=" O   LEU D 188 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148
      removed outlier: 3.938A  pdb=" N   THR D 238 " --> pdb=" O   GLN D 231 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'R' and resid 219 through 223

    508 hydrogen bonds defined for protein.
    1410 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: 1.71

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1737
        1.33 -     1.45: 2748
        1.45 -     1.58: 4719
        1.58 -     1.70: 0
        1.70 -     1.82: 92
  Bond restraints: 9296
  Sorted by residual:
  bond pdb=" CG  HIS D  35 "
       pdb=" CD2 HIS D  35 "
    ideal  model  delta    sigma   weight residual
    1.354  1.304  0.050 1.10e-02 8.26e+03 2.11e+01
  bond pdb=" CA  SER B 116 "
       pdb=" CB  SER B 116 "
    ideal  model  delta    sigma   weight residual
    1.532  1.451  0.081 1.79e-02 3.12e+03 2.07e+01
  bond pdb=" CE1 HIS D  35 "
       pdb=" NE2 HIS D  35 "
    ideal  model  delta    sigma   weight residual
    1.321  1.284  0.037 1.00e-02 1.00e+04 1.37e+01
  bond pdb=" CA  SER B 102 "
       pdb=" CB  SER B 102 "
    ideal  model  delta    sigma   weight residual
    1.529  1.479  0.050 1.74e-02 3.30e+03 8.39e+00
  bond pdb=" CA  SER B 349 "
       pdb=" CB  SER B 349 "
    ideal  model  delta    sigma   weight residual
    1.534  1.483  0.050 1.76e-02 3.23e+03 8.23e+00
  ... (remaining 9291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 11908
        2.37 -     4.75: 608
        4.75 -     7.12: 63
        7.12 -     9.49: 13
        9.49 -    11.86: 1
  Bond angle restraints: 12593
  Sorted by residual:
  angle pdb=" CA  THR B  83 "
        pdb=" CB  THR B  83 "
        pdb=" OG1 THR B  83 "
      ideal   model   delta    sigma   weight residual
     109.60   97.74   11.86 1.50e+00 4.44e-01 6.26e+01
  angle pdb=" CA  ASP A 350 "
        pdb=" CB  ASP A 350 "
        pdb=" CG  ASP A 350 "
      ideal   model   delta    sigma   weight residual
     112.60  118.64   -6.04 1.00e+00 1.00e+00 3.64e+01
  angle pdb=" CA  TRP B 357 "
        pdb=" C   TRP B 357 "
        pdb=" O   TRP B 357 "
      ideal   model   delta    sigma   weight residual
     121.78  114.49    7.29 1.28e+00 6.10e-01 3.25e+01
  angle pdb=" CA  ASP R 227 "
        pdb=" CB  ASP R 227 "
        pdb=" CG  ASP R 227 "
      ideal   model   delta    sigma   weight residual
     112.60  117.74   -5.14 1.00e+00 1.00e+00 2.64e+01
  angle pdb=" CA  THR B 120 "
        pdb=" CB  THR B 120 "
        pdb=" OG1 THR B 120 "
      ideal   model   delta    sigma   weight residual
     109.60  102.19    7.41 1.50e+00 4.44e-01 2.44e+01
  ... (remaining 12588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.34: 5185
       15.34 -    30.68: 252
       30.68 -    46.02: 48
       46.02 -    61.36: 20
       61.36 -    76.70: 10
  Dihedral angle restraints: 5515
    sinusoidal: 2136
      harmonic: 3379
  Sorted by residual:
  dihedral pdb=" CA  ALA A 326 "
           pdb=" C   ALA A 326 "
           pdb=" N   THR A 327 "
           pdb=" CA  THR A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.60   40.40     0      5.00e+00 4.00e-02 6.53e+01
  dihedral pdb=" CB  CYS R 393 "
           pdb=" SG  CYS R 393 "
           pdb=" SG  CYS R 395 "
           pdb=" CB  CYS R 395 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.12   71.12     1      1.00e+01 1.00e-02 6.49e+01
  dihedral pdb=" CA  THR A 324 "
           pdb=" C   THR A 324 "
           pdb=" N   CYS A 325 "
           pdb=" CA  CYS A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.95   36.05     0      5.00e+00 4.00e-02 5.20e+01
  ... (remaining 5512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 832
       0.053 -    0.105: 439
       0.105 -    0.157: 123
       0.157 -    0.210: 36
       0.210 -    0.262: 5
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" CB  VAL B 108 "
            pdb=" CA  VAL B 108 "
            pdb=" CG1 VAL B 108 "
            pdb=" CG2 VAL B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  ILE D 100 "
            pdb=" CA  ILE D 100 "
            pdb=" CG1 ILE D 100 "
            pdb=" CG2 ILE D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ARG A 205 "
            pdb=" N   ARG A 205 "
            pdb=" C   ARG A 205 "
            pdb=" CB  ARG A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1432 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 355 "   -0.024 2.00e-02 2.50e+03   4.84e-02 2.34e+01
        pdb=" C   LYS B 355 "    0.084 2.00e-02 2.50e+03
        pdb=" O   LYS B 355 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ILE B 356 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 357 "    0.021 2.00e-02 2.50e+03   4.41e-02 1.95e+01
        pdb=" C   TRP B 357 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   TRP B 357 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ASN B 358 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 346 "   -0.021 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   ALA B 346 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA B 346 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   THR B 347 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 207
        2.69 -     3.24: 8713
        3.24 -     3.80: 14479
        3.80 -     4.35: 20360
        4.35 -     4.90: 33371
  Nonbonded interactions: 77130
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN R 250 "
            pdb=" OH  TYR R 340 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" N   THR B  83 "
            pdb=" OG1 THR B  83 "
     model   vdw
     2.162 2.496
  nonbonded pdb=" O   PHE A 259 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR B 292 "
            pdb=" O   VAL B 333 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ILE B  76 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.251 3.040
  ... (remaining 77125 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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   0.081   9300  Z= 0.563
  Angle     :  1.224  11.864  12601  Z= 0.783
  Chirality :  0.068   0.262   1435
  Planarity :  0.011   0.158   1586
  Dihedral  : 10.502  76.699   3323
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.81 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.23), residues: 1143
  helix:  1.44 (0.23), residues: 411
  sheet:  0.17 (0.30), residues: 284
  loop : -0.23 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG B  86 
 TYR   0.039   0.005   TYR D  50 
 PHE   0.032   0.004   PHE B 353 
 TRP   0.044   0.009   TRP B 350 
 HIS   0.013   0.003   HIS B 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00906 /  0.56 ( 9296)
  covalent geometry    : angle       1.21770 /  0.78 (12593)
  SS BOND              : bond        0.02828 /  1.34 (    4)
  SS BOND              : angle       4.98001 /  2.65 (    8)
  hydrogen bonds       : bond        0.17246 / 11.75 (  498)
  hydrogen bonds       : angle       7.11407 /  5.01 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 343
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   23 LEU cc_start: 0.8700 (mt) cc_final: 0.8227 (mp)
REVERT: A  243 MET cc_start: 0.8877 (mmm) cc_final: 0.8671 (tpp)
REVERT: A  256 ASN cc_start: 0.7969 (t0) cc_final: 0.7705 (t0)
REVERT: A  281 SER cc_start: 0.8070 (m) cc_final: 0.7763 (t)
REVERT: A  283 LEU cc_start: 0.9141 (tp) cc_final: 0.8871 (tp)
REVERT: A  354 PHE cc_start: 0.8512 (t80) cc_final: 0.8251 (t80)
REVERT: B  119 MET cc_start: 0.8283 (mtp) cc_final: 0.8075 (mtp)
REVERT: C   11 GLN cc_start: 0.9293 (tp40) cc_final: 0.9058 (mp10)
REVERT: C   18 GLN cc_start: 0.9007 (tp40) cc_final: 0.8234 (tp-100)
REVERT: D   14 PRO cc_start: 0.8442 (Cg_exo) cc_final: 0.7833 (Cg_endo)
REVERT: D   90 ASP cc_start: 0.7627 (m-30) cc_final: 0.7343 (m-30)
REVERT: D  199 VAL cc_start: 0.8848 (t) cc_final: 0.8633 (t)
REVERT: R   71 ASP cc_start: 0.8577 (p0) cc_final: 0.8291 (p0)
REVERT: R  109 LEU cc_start: 0.8914 (tp) cc_final: 0.8414 (mt)
REVERT: R  124 ASP cc_start: 0.9097 (m-30) cc_final: 0.8684 (m-30)
REVERT: R  186 PHE cc_start: 0.8452 (m-10) cc_final: 0.8170 (p90)
REVERT: R  194 ARG cc_start: 0.6242 (mtt180) cc_final: 0.6001 (mtt90)
REVERT: R  219 MET cc_start: 0.9155 (mmp) cc_final: 0.8662 (tpp)
REVERT: R  223 ASN cc_start: 0.7835 (t0) cc_final: 0.7610 (t0)
REVERT: R  255 MET cc_start: 0.8966 (mmm) cc_final: 0.8624 (mmm)
REVERT: R  327 CYS cc_start: 0.7751 (m) cc_final: 0.7451 (m)
REVERT: R  332 HIS cc_start: 0.7833 (m-70) cc_final: 0.7304 (m90)
REVERT: R  335 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8404 (mtp-110)
REVERT: R  359 MET cc_start: 0.8996 (mtt) cc_final: 0.8671 (tmm)
REVERT: R  382 ASN cc_start: 0.9010 (m110) cc_final: 0.8794 (m-40)
REVERT: R  383 PHE cc_start: 0.8289 (t80) cc_final: 0.8033 (t80)
REVERT: L   12 ILE cc_start: 0.8784 (mm) cc_final: 0.8443 (mm)
REVERT: L   13 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6209 (tp)
  outliers start: 6
  outliers final: 3
  residues processed: 347
  average time/residue: 0.1104
  time to fit residues: 50.5165
Evaluate side-chains
  213 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 209
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain R residue  395 CYS
Chi-restraints excluded: chain L residue   13 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 195 HIS
B  62 GLN
D  82 GLN
R  93 ASN
R 114 HIS
R 138 ASN
R 312 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.103018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.071681 restraints weight = 24259.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.86
r_work: 0.3056 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9300  Z= 0.181
  Angle     :  0.659   8.807  12601  Z= 0.352
  Chirality :  0.044   0.160   1435
  Planarity :  0.005   0.043   1586
  Dihedral  :  4.721  33.047   1264
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 10.35 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.24), residues: 1143
  helix:  1.86 (0.24), residues: 412
  sheet:  0.27 (0.31), residues: 279
  loop : -0.28 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 311 
 TYR   0.018   0.002   TYR D 103 
 PHE   0.040   0.002   PHE R 349 
 TRP   0.019   0.002   TRP B 187 
 HIS   0.004   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.18 ( 9296)
  covalent geometry    : angle       0.65773 /  0.35 (12593)
  SS BOND              : bond        0.00291 /  0.14 (    4)
  SS BOND              : angle       1.91668 /  1.13 (    8)
  hydrogen bonds       : bond        0.04756 /  3.19 (  498)
  hydrogen bonds       : angle       5.48722 /  3.85 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 232
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   25 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8605 (tm-30)
REVERT: A  229 ASP cc_start: 0.8856 (m-30) cc_final: 0.8395 (t70)
REVERT: A  256 ASN cc_start: 0.8368 (t0) cc_final: 0.7844 (t0)
REVERT: A  302 TYR cc_start: 0.9043 (t80) cc_final: 0.8742 (t80)
REVERT: A  354 PHE cc_start: 0.8895 (t80) cc_final: 0.8652 (t80)
REVERT: B   41 LYS cc_start: 0.9650 (tttt) cc_final: 0.9390 (ptpp)
REVERT: B   70 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8005 (ptp-110)
REVERT: B  235 MET cc_start: 0.8708 (ptm) cc_final: 0.7526 (ppp)
REVERT: B  244 GLU cc_start: 0.8295 (mp0) cc_final: 0.7995 (mp0)
REVERT: B  280 MET cc_start: 0.8426 (tpp) cc_final: 0.8139 (mmm)
REVERT: B  282 TYR cc_start: 0.9022 (m-80) cc_final: 0.8675 (m-80)
REVERT: B  298 LYS cc_start: 0.9387 (tttp) cc_final: 0.9005 (tttm)
REVERT: B  310 PHE cc_start: 0.9197 (m-10) cc_final: 0.8790 (m-10)
REVERT: C   17 GLU cc_start: 0.9408 (pt0) cc_final: 0.9159 (pp20)
REVERT: C   21 MET cc_start: 0.9041 (tmm) cc_final: 0.8760 (ttt)
REVERT: C   42 GLU cc_start: 0.8956 (pp20) cc_final: 0.8752 (pp20)
REVERT: C   47 GLU cc_start: 0.9035 (tp30) cc_final: 0.8717 (tp30)
REVERT: D   73 ASP cc_start: 0.7283 (t0) cc_final: 0.6845 (t0)
REVERT: D   94 TYR cc_start: 0.8701 (m-80) cc_final: 0.8152 (m-80)
REVERT: D  186 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7763 (mm-40)
REVERT: D  244 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8609 (ttmm)
REVERT: R   71 ASP cc_start: 0.8741 (p0) cc_final: 0.8458 (p0)
REVERT: R  128 LEU cc_start: 0.9115 (mt) cc_final: 0.8064 (tp)
REVERT: R  255 MET cc_start: 0.9054 (mmm) cc_final: 0.8603 (mmm)
REVERT: R  332 HIS cc_start: 0.8165 (m-70) cc_final: 0.7281 (m90)
REVERT: R  335 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8363 (mtm-85)
REVERT: R  352 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8762 (p0)
  outliers start: 28
  outliers final: 15
  residues processed: 247
  average time/residue: 0.1098
  time to fit residues: 35.9475
Evaluate side-chains
  212 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain R residue  138 ASN
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  352 ASP
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    0.0470
   chunk 5 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 104 optimal weight:   30.0000
   chunk 101 optimal weight:   20.0000
   chunk 12 optimal weight:    0.6980
   chunk 108 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    2.7484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
D 183 GLN
R 138 ASN
R 382 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.101662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.071268 restraints weight = 24239.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.82
r_work: 0.3066 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9300  Z= 0.155
  Angle     :  0.626   7.946  12601  Z= 0.326
  Chirality :  0.043   0.142   1435
  Planarity :  0.004   0.043   1586
  Dihedral  :  4.401  29.123   1259
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.66 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1143
  helix:  1.99 (0.25), residues: 414
  sheet:  0.22 (0.31), residues: 285
  loop : -0.20 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 311 
 TYR   0.018   0.002   TYR R 331 
 PHE   0.020   0.001   PHE R 349 
 TRP   0.017   0.002   TRP B 187 
 HIS   0.005   0.001   HIS R 114 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 9296)
  covalent geometry    : angle       0.62407 /  0.33 (12593)
  SS BOND              : bond        0.00236 /  0.10 (    4)
  SS BOND              : angle       1.79460 /  1.01 (    8)
  hydrogen bonds       : bond        0.04253 /  2.87 (  498)
  hydrogen bonds       : angle       5.25803 /  3.67 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   32 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8604 (ttm-80)
REVERT: A  229 ASP cc_start: 0.8759 (m-30) cc_final: 0.8390 (t70)
REVERT: A  242 ARG cc_start: 0.9087 (mtt90) cc_final: 0.8662 (tpp80)
REVERT: A  252 SER cc_start: 0.9536 (t) cc_final: 0.9180 (p)
REVERT: A  256 ASN cc_start: 0.8367 (t0) cc_final: 0.7688 (t0)
REVERT: A  302 TYR cc_start: 0.8939 (t80) cc_final: 0.8623 (t80)
REVERT: A  313 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.8142 (ptp-110)
REVERT: B   41 LYS cc_start: 0.9611 (tttt) cc_final: 0.9351 (ptpp)
REVERT: B  235 MET cc_start: 0.8794 (ptm) cc_final: 0.7947 (ppp)
REVERT: B  244 GLU cc_start: 0.8345 (mp0) cc_final: 0.7959 (mp0)
REVERT: B  282 TYR cc_start: 0.8970 (m-80) cc_final: 0.8592 (m-80)
REVERT: B  298 LYS cc_start: 0.9380 (tttp) cc_final: 0.8905 (tttm)
REVERT: B  310 PHE cc_start: 0.9247 (m-10) cc_final: 0.8926 (m-80)
REVERT: C   11 GLN cc_start: 0.9532 (tp40) cc_final: 0.9218 (mp10)
REVERT: C   15 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9198 (pp)
REVERT: C   21 MET cc_start: 0.8875 (tmm) cc_final: 0.8654 (ttt)
REVERT: C   42 GLU cc_start: 0.9008 (pp20) cc_final: 0.8781 (pp20)
REVERT: C   47 GLU cc_start: 0.9128 (tp30) cc_final: 0.8802 (tp30)
REVERT: D   43 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8792 (mmmm)
REVERT: D   73 ASP cc_start: 0.7388 (t0) cc_final: 0.6886 (t0)
REVERT: D   87 ARG cc_start: 0.7872 (mpp80) cc_final: 0.7479 (mpp80)
REVERT: D   90 ASP cc_start: 0.8871 (m-30) cc_final: 0.8650 (m-30)
REVERT: D   93 MET cc_start: 0.8390 (tpp) cc_final: 0.7976 (tpp)
REVERT: D   94 TYR cc_start: 0.8677 (m-80) cc_final: 0.8061 (m-80)
REVERT: D  186 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7735 (mm-40)
REVERT: D  218 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8734 (mmm-85)
REVERT: R   71 ASP cc_start: 0.8720 (p0) cc_final: 0.8430 (p0)
REVERT: R  128 LEU cc_start: 0.9286 (mt) cc_final: 0.8219 (tp)
REVERT: R  148 PHE cc_start: 0.8891 (m-80) cc_final: 0.8656 (m-80)
REVERT: R  205 TRP cc_start: 0.7868 (m100) cc_final: 0.7466 (t60)
REVERT: R  219 MET cc_start: 0.8542 (mmm) cc_final: 0.7410 (tpp)
REVERT: R  255 MET cc_start: 0.9114 (mmm) cc_final: 0.8651 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 228
  average time/residue: 0.1175
  time to fit residues: 35.3578
Evaluate side-chains
  216 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  379 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
D 183 GLN
R 382 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.103676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.074867 restraints weight = 24323.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 3.69
r_work: 0.3151 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9300  Z= 0.133
  Angle     :  0.602  12.021  12601  Z= 0.314
  Chirality :  0.042   0.137   1435
  Planarity :  0.004   0.044   1586
  Dihedral  :  4.246  27.755   1258
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.57 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1143
  helix:  1.97 (0.25), residues: 415
  sheet:  0.11 (0.31), residues: 290
  loop : -0.09 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 334 
 TYR   0.019   0.001   TYR A 296 
 PHE   0.015   0.001   PHE A 259 
 TRP   0.016   0.001   TRP B 187 
 HIS   0.003   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 9296)
  covalent geometry    : angle       0.60102 /  0.31 (12593)
  SS BOND              : bond        0.00256 /  0.12 (    4)
  SS BOND              : angle       1.66727 /  0.98 (    8)
  hydrogen bonds       : bond        0.03906 /  2.60 (  498)
  hydrogen bonds       : angle       5.08988 /  3.55 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   32 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8597 (ttm-80)
REVERT: A  229 ASP cc_start: 0.8747 (m-30) cc_final: 0.8538 (t70)
REVERT: A  242 ARG cc_start: 0.9108 (mtt90) cc_final: 0.8726 (tpp80)
REVERT: A  243 MET cc_start: 0.8775 (mmt) cc_final: 0.8199 (mmm)
REVERT: A  252 SER cc_start: 0.9478 (t) cc_final: 0.9121 (p)
REVERT: A  256 ASN cc_start: 0.8457 (t0) cc_final: 0.7836 (t0)
REVERT: A  302 TYR cc_start: 0.9062 (t80) cc_final: 0.8492 (t80)
REVERT: A  306 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8136 (mm-40)
REVERT: A  313 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.7868 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8091 (ttmm)
REVERT: B   41 LYS cc_start: 0.9589 (tttt) cc_final: 0.9375 (ptpp)
REVERT: B  235 MET cc_start: 0.8790 (ptm) cc_final: 0.7579 (ppp)
REVERT: B  244 GLU cc_start: 0.8387 (mp0) cc_final: 0.7999 (mp0)
REVERT: B  282 TYR cc_start: 0.8946 (m-80) cc_final: 0.8562 (m-80)
REVERT: B  298 LYS cc_start: 0.9370 (tttp) cc_final: 0.8781 (tttm)
REVERT: B  310 PHE cc_start: 0.9218 (m-10) cc_final: 0.8958 (m-80)
REVERT: B  326 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8254 (tp)
REVERT: C   11 GLN cc_start: 0.9510 (tp40) cc_final: 0.9222 (mp10)
REVERT: C   15 LEU cc_start: 0.9536 (tt) cc_final: 0.9184 (pp)
REVERT: C   22 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8503 (mt-10)
REVERT: C   42 GLU cc_start: 0.8995 (pp20) cc_final: 0.8732 (pp20)
REVERT: D   34 MET cc_start: 0.8791 (mmm) cc_final: 0.8539 (mmm)
REVERT: D   43 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8965 (mmmt)
REVERT: D   73 ASP cc_start: 0.7600 (t0) cc_final: 0.7108 (t0)
REVERT: D   87 ARG cc_start: 0.8215 (mpp80) cc_final: 0.7873 (mpp80)
REVERT: D   93 MET cc_start: 0.8563 (tpp) cc_final: 0.8100 (tpp)
REVERT: D   94 TYR cc_start: 0.8680 (m-80) cc_final: 0.7983 (m-80)
REVERT: D  186 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7806 (mm-40)
REVERT: D  218 ARG cc_start: 0.8948 (mmm-85) cc_final: 0.8697 (mmm-85)
REVERT: R   71 ASP cc_start: 0.8694 (p0) cc_final: 0.8419 (p0)
REVERT: R  128 LEU cc_start: 0.9357 (mt) cc_final: 0.8553 (tp)
REVERT: R  161 ASP cc_start: 0.9420 (m-30) cc_final: 0.9116 (m-30)
REVERT: R  205 TRP cc_start: 0.7978 (m100) cc_final: 0.7506 (t60)
REVERT: R  255 MET cc_start: 0.9108 (mmm) cc_final: 0.8640 (mmm)
REVERT: R  261 MET cc_start: 0.8033 (ptt) cc_final: 0.7767 (ptt)
REVERT: R  335 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8135 (mtm-85)
REVERT: R  337 MET cc_start: 0.6982 (mmp) cc_final: 0.6642 (mmp)
  outliers start: 23
  outliers final: 14
  residues processed: 224
  average time/residue: 0.1132
  time to fit residues: 33.1770
Evaluate side-chains
  210 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 195
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 79 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 60 optimal weight:   40.0000
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
R  93 ASN
R 382 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.103521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.074701 restraints weight = 24432.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 3.71
r_work: 0.3170 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.5047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9300  Z= 0.130
  Angle     :  0.617  10.402  12601  Z= 0.316
  Chirality :  0.043   0.179   1435
  Planarity :  0.004   0.043   1586
  Dihedral  :  4.111  20.423   1258
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.48 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.25), residues: 1143
  helix:  1.95 (0.25), residues: 418
  sheet:  0.06 (0.30), residues: 292
  loop : -0.15 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 334 
 TYR   0.016   0.001   TYR R 331 
 PHE   0.014   0.001   PHE A 259 
 TRP   0.016   0.001   TRP B 100 
 HIS   0.014   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 9296)
  covalent geometry    : angle       0.61618 /  0.32 (12593)
  SS BOND              : bond        0.00269 /  0.13 (    4)
  SS BOND              : angle       1.57572 /  0.93 (    8)
  hydrogen bonds       : bond        0.03719 /  2.49 (  498)
  hydrogen bonds       : angle       4.97732 /  3.47 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   25 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8336 (tp30)
REVERT: A   28 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: A   32 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8632 (ttm-80)
REVERT: A  242 ARG cc_start: 0.9102 (mtt90) cc_final: 0.8728 (tpp80)
REVERT: A  243 MET cc_start: 0.8761 (mmt) cc_final: 0.8164 (mmm)
REVERT: A  252 SER cc_start: 0.9402 (t) cc_final: 0.8990 (p)
REVERT: A  255 ASN cc_start: 0.9154 (t160) cc_final: 0.8746 (m110)
REVERT: A  256 ASN cc_start: 0.8518 (t0) cc_final: 0.7885 (t0)
REVERT: A  281 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (t)
REVERT: A  302 TYR cc_start: 0.9130 (t80) cc_final: 0.8576 (t80)
REVERT: A  306 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8141 (mm-40)
REVERT: A  312 LYS cc_start: 0.9204 (mmtm) cc_final: 0.8703 (mmtt)
REVERT: A  313 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.7980 (mtm180)
REVERT: A  317 LYS cc_start: 0.8490 (ttmm) cc_final: 0.7609 (mtpt)
REVERT: A  325 CYS cc_start: 0.8263 (m) cc_final: 0.6633 (p)
REVERT: B   41 LYS cc_start: 0.9603 (tttt) cc_final: 0.9385 (ptpp)
REVERT: B  235 MET cc_start: 0.8674 (ptm) cc_final: 0.7534 (ppp)
REVERT: B  244 GLU cc_start: 0.8426 (mp0) cc_final: 0.7973 (mp0)
REVERT: B  280 MET cc_start: 0.8078 (mmm) cc_final: 0.7755 (mmm)
REVERT: B  282 TYR cc_start: 0.8958 (m-80) cc_final: 0.8680 (m-80)
REVERT: B  298 LYS cc_start: 0.9227 (tttp) cc_final: 0.8820 (tttm)
REVERT: B  310 PHE cc_start: 0.9172 (m-10) cc_final: 0.8927 (m-80)
REVERT: C   11 GLN cc_start: 0.9502 (tp40) cc_final: 0.9226 (mp10)
REVERT: C   15 LEU cc_start: 0.9541 (tt) cc_final: 0.9198 (pp)
REVERT: C   21 MET cc_start: 0.9156 (ttt) cc_final: 0.8944 (ttm)
REVERT: C   26 ASP cc_start: 0.9548 (m-30) cc_final: 0.9193 (t0)
REVERT: C   42 GLU cc_start: 0.8994 (pp20) cc_final: 0.8716 (pp20)
REVERT: C   47 GLU cc_start: 0.9068 (tp30) cc_final: 0.8861 (tp30)
REVERT: D   43 LYS cc_start: 0.9319 (mmmm) cc_final: 0.9018 (mmmm)
REVERT: D   73 ASP cc_start: 0.7660 (t0) cc_final: 0.7151 (t0)
REVERT: D   87 ARG cc_start: 0.8255 (mpp80) cc_final: 0.7893 (mpp80)
REVERT: D   93 MET cc_start: 0.8653 (tpp) cc_final: 0.8319 (tpp)
REVERT: D   94 TYR cc_start: 0.8741 (m-80) cc_final: 0.8401 (m-10)
REVERT: D  186 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7710 (mm-40)
REVERT: R   71 ASP cc_start: 0.8651 (p0) cc_final: 0.8338 (p0)
REVERT: R  128 LEU cc_start: 0.9320 (mt) cc_final: 0.8539 (tp)
REVERT: R  199 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6295 (mmtm)
REVERT: R  205 TRP cc_start: 0.8084 (m100) cc_final: 0.7580 (t60)
REVERT: R  255 MET cc_start: 0.9111 (mmm) cc_final: 0.8621 (mmm)
REVERT: R  261 MET cc_start: 0.8032 (ptt) cc_final: 0.7787 (ptt)
REVERT: R  335 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8328 (mtp-110)
REVERT: R  337 MET cc_start: 0.6984 (mmp) cc_final: 0.6645 (mmp)
  outliers start: 24
  outliers final: 14
  residues processed: 216
  average time/residue: 0.1041
  time to fit residues: 29.8886
Evaluate side-chains
  204 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 108 optimal weight:   20.0000
   chunk 72 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   overall best weight:    5.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.070543 restraints weight = 24750.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 3.68
r_work: 0.3076 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9300  Z= 0.223
  Angle     :  0.671  10.201  12601  Z= 0.350
  Chirality :  0.045   0.149   1435
  Planarity :  0.004   0.044   1586
  Dihedral  :  4.359  18.029   1258
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.98 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.25), residues: 1143
  helix:  1.73 (0.25), residues: 419
  sheet: -0.22 (0.30), residues: 286
  loop : -0.42 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 208 
 TYR   0.014   0.002   TYR D 190 
 PHE   0.015   0.002   PHE A 259 
 TRP   0.025   0.002   TRP B 357 
 HIS   0.010   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.22 ( 9296)
  covalent geometry    : angle       0.66980 /  0.35 (12593)
  SS BOND              : bond        0.00222 /  0.11 (    4)
  SS BOND              : angle       1.50786 /  0.91 (    8)
  hydrogen bonds       : bond        0.04081 /  2.69 (  498)
  hydrogen bonds       : angle       5.11090 /  3.56 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   32 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8604 (ttm-80)
REVERT: A  243 MET cc_start: 0.8741 (mmt) cc_final: 0.7942 (mmm)
REVERT: A  252 SER cc_start: 0.9451 (t) cc_final: 0.9107 (p)
REVERT: A  256 ASN cc_start: 0.8595 (t0) cc_final: 0.8039 (t0)
REVERT: A  281 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7666 (t)
REVERT: A  302 TYR cc_start: 0.9169 (t80) cc_final: 0.8523 (t80)
REVERT: A  306 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8199 (mm-40)
REVERT: A  313 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.7962 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7908 (mtmt)
REVERT: A  320 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7807 (m-80)
REVERT: A  325 CYS cc_start: 0.8246 (m) cc_final: 0.7527 (p)
REVERT: B   41 LYS cc_start: 0.9592 (tttt) cc_final: 0.9353 (ptpp)
REVERT: B  190 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: B  235 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7477 (ppp)
REVERT: B  244 GLU cc_start: 0.8498 (mp0) cc_final: 0.8043 (mp0)
REVERT: B  280 MET cc_start: 0.8110 (mmm) cc_final: 0.7765 (mmm)
REVERT: B  282 TYR cc_start: 0.8931 (m-80) cc_final: 0.8572 (m-80)
REVERT: B  293 SER cc_start: 0.8432 (p) cc_final: 0.8218 (m)
REVERT: B  298 LYS cc_start: 0.9375 (tttp) cc_final: 0.8796 (tttm)
REVERT: B  310 PHE cc_start: 0.9223 (m-10) cc_final: 0.8985 (m-80)
REVERT: C   11 GLN cc_start: 0.9549 (tp40) cc_final: 0.9258 (mp10)
REVERT: C   13 ARG cc_start: 0.9315 (ptp-170) cc_final: 0.9013 (ptp90)
REVERT: C   15 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9272 (pp)
REVERT: C   20 LYS cc_start: 0.9129 (pttm) cc_final: 0.8777 (ptpp)
REVERT: C   26 ASP cc_start: 0.9520 (m-30) cc_final: 0.9224 (t0)
REVERT: C   42 GLU cc_start: 0.9201 (pp20) cc_final: 0.8938 (pp20)
REVERT: D   43 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9004 (mmmm)
REVERT: D   73 ASP cc_start: 0.7723 (t0) cc_final: 0.7210 (t0)
REVERT: D   87 ARG cc_start: 0.8064 (mpp80) cc_final: 0.7669 (mpp80)
REVERT: D   89 GLU cc_start: 0.9032 (pm20) cc_final: 0.8543 (pm20)
REVERT: D   93 MET cc_start: 0.8702 (tpp) cc_final: 0.8247 (tpp)
REVERT: D  186 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7785 (mm-40)
REVERT: R   71 ASP cc_start: 0.8776 (p0) cc_final: 0.8493 (p0)
REVERT: R  128 LEU cc_start: 0.9431 (mt) cc_final: 0.8696 (tt)
REVERT: R  205 TRP cc_start: 0.8084 (m100) cc_final: 0.7510 (t60)
REVERT: R  255 MET cc_start: 0.9137 (mmm) cc_final: 0.8681 (mmm)
REVERT: R  261 MET cc_start: 0.7662 (ptt) cc_final: 0.7435 (ptt)
REVERT: R  337 MET cc_start: 0.7008 (mmp) cc_final: 0.6732 (mmp)
  outliers start: 30
  outliers final: 16
  residues processed: 207
  average time/residue: 0.1064
  time to fit residues: 29.3408
Evaluate side-chains
  203 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 82 optimal weight:   40.0000
   chunk 18 optimal weight:    0.6980
   chunk 72 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    3.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.100949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.072534 restraints weight = 24915.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 3.78
r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.5525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9300  Z= 0.153
  Angle     :  0.652  13.428  12601  Z= 0.332
  Chirality :  0.043   0.153   1435
  Planarity :  0.004   0.044   1586
  Dihedral  :  4.167  17.071   1258
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.69 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1143
  helix:  1.83 (0.25), residues: 419
  sheet: -0.21 (0.29), residues: 289
  loop : -0.40 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.013   0.001   TYR R 331 
 PHE   0.020   0.001   PHE A 259 
 TRP   0.015   0.002   TRP B 187 
 HIS   0.007   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 9296)
  covalent geometry    : angle       0.65072 /  0.33 (12593)
  SS BOND              : bond        0.00253 /  0.12 (    4)
  SS BOND              : angle       1.54245 /  0.92 (    8)
  hydrogen bonds       : bond        0.03729 /  2.46 (  498)
  hydrogen bonds       : angle       5.00386 /  3.49 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 192
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   25 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8264 (tp30)
REVERT: A   26 ASP cc_start: 0.8902 (p0) cc_final: 0.8680 (p0)
REVERT: A   28 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: A  207 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8047 (mm-30)
REVERT: A  252 SER cc_start: 0.9381 (t) cc_final: 0.8989 (p)
REVERT: A  255 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8741 (m110)
REVERT: A  256 ASN cc_start: 0.8494 (t0) cc_final: 0.7953 (t0)
REVERT: A  281 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  302 TYR cc_start: 0.9208 (t80) cc_final: 0.8549 (t80)
REVERT: A  306 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8212 (mm-40)
REVERT: A  312 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8616 (mmtt)
REVERT: A  313 ARG cc_start: 0.8255 (ptp-110) cc_final: 0.7592 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8036 (mtmt)
REVERT: A  320 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (m-10)
REVERT: A  325 CYS cc_start: 0.8228 (m) cc_final: 0.7993 (p)
REVERT: B   41 LYS cc_start: 0.9612 (tttt) cc_final: 0.9379 (ptpp)
REVERT: B  190 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: B  244 GLU cc_start: 0.8503 (mp0) cc_final: 0.8008 (mp0)
REVERT: B  280 MET cc_start: 0.8453 (mmm) cc_final: 0.8145 (mmm)
REVERT: B  282 TYR cc_start: 0.9046 (m-80) cc_final: 0.8774 (m-80)
REVERT: B  298 LYS cc_start: 0.9274 (tttp) cc_final: 0.8869 (tttm)
REVERT: B  310 PHE cc_start: 0.9174 (m-10) cc_final: 0.8930 (m-80)
REVERT: C   11 GLN cc_start: 0.9509 (tp40) cc_final: 0.9222 (mp10)
REVERT: C   15 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9288 (pp)
REVERT: C   26 ASP cc_start: 0.9532 (m-30) cc_final: 0.9190 (t0)
REVERT: C   29 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7854 (mmmt)
REVERT: C   42 GLU cc_start: 0.9213 (pp20) cc_final: 0.8924 (pp20)
REVERT: C   46 LYS cc_start: 0.9321 (mmmt) cc_final: 0.8907 (tppt)
REVERT: D   43 LYS cc_start: 0.9294 (mmmm) cc_final: 0.8958 (mmmm)
REVERT: D   46 GLU cc_start: 0.8071 (tt0) cc_final: 0.7869 (tt0)
REVERT: D   73 ASP cc_start: 0.7574 (t0) cc_final: 0.7089 (t0)
REVERT: D   87 ARG cc_start: 0.8452 (mpp80) cc_final: 0.8013 (mpp80)
REVERT: D   89 GLU cc_start: 0.9102 (pm20) cc_final: 0.8711 (pm20)
REVERT: D   90 ASP cc_start: 0.8910 (m-30) cc_final: 0.8012 (m-30)
REVERT: D   93 MET cc_start: 0.8773 (tpp) cc_final: 0.8233 (tpp)
REVERT: D   94 TYR cc_start: 0.8770 (m-80) cc_final: 0.8311 (m-80)
REVERT: D  186 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7783 (mm-40)
REVERT: R   71 ASP cc_start: 0.8797 (p0) cc_final: 0.8525 (p0)
REVERT: R  128 LEU cc_start: 0.9211 (mt) cc_final: 0.8443 (tt)
REVERT: R  205 TRP cc_start: 0.8098 (m100) cc_final: 0.7587 (t60)
REVERT: R  219 MET cc_start: 0.7079 (mmm) cc_final: 0.6552 (mmm)
REVERT: R  255 MET cc_start: 0.9163 (mmm) cc_final: 0.8709 (mmm)
REVERT: R  261 MET cc_start: 0.7604 (ptt) cc_final: 0.7292 (ptt)
REVERT: R  337 MET cc_start: 0.7098 (mmp) cc_final: 0.6895 (mmp)
  outliers start: 29
  outliers final: 20
  residues processed: 203
  average time/residue: 0.1093
  time to fit residues: 29.5051
Evaluate side-chains
  204 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  357 TRP
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain R residue  103 LYS
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 104 optimal weight:   30.0000
   chunk 91 optimal weight:    7.9990
   overall best weight:    3.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.100491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.072055 restraints weight = 25128.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.80
r_work: 0.3078 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9300  Z= 0.171
  Angle     :  0.673  15.381  12601  Z= 0.347
  Chirality :  0.044   0.185   1435
  Planarity :  0.004   0.044   1586
  Dihedral  :  4.185  17.323   1258
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.59 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.25), residues: 1143
  helix:  1.76 (0.25), residues: 420
  sheet: -0.19 (0.30), residues: 286
  loop : -0.40 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 218 
 TYR   0.014   0.002   TYR R 366 
 PHE   0.017   0.001   PHE A 259 
 TRP   0.015   0.002   TRP B 187 
 HIS   0.006   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.17 ( 9296)
  covalent geometry    : angle       0.67217 /  0.35 (12593)
  SS BOND              : bond        0.00231 /  0.11 (    4)
  SS BOND              : angle       1.50592 /  0.91 (    8)
  hydrogen bonds       : bond        0.03817 /  2.52 (  498)
  hydrogen bonds       : angle       5.02888 /  3.52 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   21 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8323 (ttm-80)
REVERT: A  207 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8035 (mm-30)
REVERT: A  252 SER cc_start: 0.9358 (t) cc_final: 0.8982 (p)
REVERT: A  255 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8753 (m-40)
REVERT: A  256 ASN cc_start: 0.8393 (t0) cc_final: 0.7888 (t0)
REVERT: A  281 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7816 (t)
REVERT: A  302 TYR cc_start: 0.9218 (t80) cc_final: 0.8559 (t80)
REVERT: A  306 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8223 (mm-40)
REVERT: A  313 ARG cc_start: 0.8114 (ptp-110) cc_final: 0.7474 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8085 (mtmt)
REVERT: A  320 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8022 (m-10)
REVERT: A  325 CYS cc_start: 0.8686 (m) cc_final: 0.8116 (p)
REVERT: B   41 LYS cc_start: 0.9627 (tttt) cc_final: 0.9376 (ptpp)
REVERT: B  190 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: B  235 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7358 (ppp)
REVERT: B  244 GLU cc_start: 0.8524 (mp0) cc_final: 0.8016 (mp0)
REVERT: B  280 MET cc_start: 0.8360 (mmm) cc_final: 0.7989 (mmm)
REVERT: B  282 TYR cc_start: 0.9025 (m-80) cc_final: 0.8681 (m-80)
REVERT: B  298 LYS cc_start: 0.9284 (tttp) cc_final: 0.8871 (tttm)
REVERT: B  310 PHE cc_start: 0.9177 (m-10) cc_final: 0.8926 (m-80)
REVERT: C   11 GLN cc_start: 0.9503 (tp40) cc_final: 0.9226 (mp10)
REVERT: C   21 MET cc_start: 0.9319 (tmm) cc_final: 0.8990 (tmm)
REVERT: C   26 ASP cc_start: 0.9524 (m-30) cc_final: 0.9184 (t0)
REVERT: C   42 GLU cc_start: 0.9246 (pp20) cc_final: 0.8951 (pp20)
REVERT: C   46 LYS cc_start: 0.9391 (mmmt) cc_final: 0.8945 (tppt)
REVERT: D   43 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9043 (mmmm)
REVERT: D   73 ASP cc_start: 0.7530 (t0) cc_final: 0.7049 (t0)
REVERT: D   87 ARG cc_start: 0.8457 (mpp80) cc_final: 0.8200 (mpp80)
REVERT: D   89 GLU cc_start: 0.9100 (pm20) cc_final: 0.8273 (pm20)
REVERT: D   90 ASP cc_start: 0.8929 (m-30) cc_final: 0.7639 (m-30)
REVERT: D   93 MET cc_start: 0.8788 (tpp) cc_final: 0.8339 (tpp)
REVERT: D   94 TYR cc_start: 0.8759 (m-80) cc_final: 0.8316 (m-80)
REVERT: D  186 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7857 (mm-40)
REVERT: R   71 ASP cc_start: 0.8809 (p0) cc_final: 0.8537 (p0)
REVERT: R  128 LEU cc_start: 0.9318 (mt) cc_final: 0.8764 (tt)
REVERT: R  205 TRP cc_start: 0.8130 (m100) cc_final: 0.7542 (t60)
REVERT: R  255 MET cc_start: 0.9179 (mmm) cc_final: 0.8737 (mmm)
REVERT: R  261 MET cc_start: 0.7739 (ptt) cc_final: 0.7461 (ptt)
REVERT: R  337 MET cc_start: 0.7121 (mmp) cc_final: 0.6919 (mmp)
  outliers start: 28
  outliers final: 19
  residues processed: 199
  average time/residue: 0.1102
  time to fit residues: 29.2921
Evaluate side-chains
  203 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain R residue  103 LYS
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 18 optimal weight:    0.1980
   chunk 96 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    2.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.101509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.072915 restraints weight = 25059.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 3.89
r_work: 0.3117 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.5817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9300  Z= 0.145
  Angle     :  0.692  15.615  12601  Z= 0.351
  Chirality :  0.044   0.205   1435
  Planarity :  0.004   0.043   1586
  Dihedral  :  4.121  17.672   1258
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.20 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.25), residues: 1143
  helix:  1.75 (0.25), residues: 420
  sheet: -0.14 (0.30), residues: 284
  loop : -0.42 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.025   0.001   TYR R 366 
 PHE   0.017   0.001   PHE A 259 
 TRP   0.015   0.001   TRP B 187 
 HIS   0.006   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 9296)
  covalent geometry    : angle       0.69091 /  0.35 (12593)
  SS BOND              : bond        0.00261 /  0.13 (    4)
  SS BOND              : angle       1.52395 /  0.92 (    8)
  hydrogen bonds       : bond        0.03723 /  2.47 (  498)
  hydrogen bonds       : angle       5.00860 /  3.52 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   21 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8331 (ttm-80)
REVERT: A  207 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8021 (mm-30)
REVERT: A  252 SER cc_start: 0.9343 (t) cc_final: 0.8983 (p)
REVERT: A  255 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8882 (m-40)
REVERT: A  256 ASN cc_start: 0.8726 (t0) cc_final: 0.8184 (t0)
REVERT: A  281 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7786 (t)
REVERT: A  302 TYR cc_start: 0.9213 (t80) cc_final: 0.8577 (t80)
REVERT: A  306 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: A  312 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8609 (mmtt)
REVERT: A  313 ARG cc_start: 0.8179 (ptp-110) cc_final: 0.7774 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8169 (mtmt)
REVERT: A  325 CYS cc_start: 0.8708 (m) cc_final: 0.8148 (p)
REVERT: A  330 LYS cc_start: 0.9652 (mttt) cc_final: 0.9451 (mmtm)
REVERT: B   41 LYS cc_start: 0.9621 (tttt) cc_final: 0.9371 (ptpp)
REVERT: B  190 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: B  235 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7344 (ppp)
REVERT: B  244 GLU cc_start: 0.8539 (mp0) cc_final: 0.8028 (mp0)
REVERT: B  280 MET cc_start: 0.8440 (mmm) cc_final: 0.8131 (mmm)
REVERT: B  282 TYR cc_start: 0.9016 (m-80) cc_final: 0.8807 (m-80)
REVERT: B  298 LYS cc_start: 0.9363 (tttp) cc_final: 0.8934 (tttm)
REVERT: B  310 PHE cc_start: 0.9125 (m-10) cc_final: 0.8914 (m-80)
REVERT: C   11 GLN cc_start: 0.9505 (tp40) cc_final: 0.9239 (mp10)
REVERT: C   13 ARG cc_start: 0.9244 (ptp-110) cc_final: 0.8858 (ptp90)
REVERT: C   21 MET cc_start: 0.9252 (tmm) cc_final: 0.8971 (tmm)
REVERT: C   26 ASP cc_start: 0.9517 (m-30) cc_final: 0.9186 (t0)
REVERT: C   42 GLU cc_start: 0.9240 (pp20) cc_final: 0.8943 (pp20)
REVERT: C   46 LYS cc_start: 0.9363 (mmmt) cc_final: 0.8937 (tppt)
REVERT: D   43 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9036 (mmmm)
REVERT: D   73 ASP cc_start: 0.7559 (t0) cc_final: 0.7086 (t0)
REVERT: D   87 ARG cc_start: 0.8476 (mpp80) cc_final: 0.8269 (mpp80)
REVERT: D   89 GLU cc_start: 0.9092 (pm20) cc_final: 0.8364 (pm20)
REVERT: D   90 ASP cc_start: 0.8921 (m-30) cc_final: 0.7827 (m-30)
REVERT: D   93 MET cc_start: 0.8911 (tpp) cc_final: 0.8704 (tpp)
REVERT: D   94 TYR cc_start: 0.8696 (m-80) cc_final: 0.8260 (m-80)
REVERT: D  186 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7815 (mm-40)
REVERT: R   71 ASP cc_start: 0.8762 (p0) cc_final: 0.8492 (p0)
REVERT: R  128 LEU cc_start: 0.9371 (mt) cc_final: 0.8492 (tt)
REVERT: R  205 TRP cc_start: 0.8193 (m100) cc_final: 0.7630 (t60)
REVERT: R  255 MET cc_start: 0.9203 (mmm) cc_final: 0.8697 (mmm)
REVERT: R  261 MET cc_start: 0.7759 (ptt) cc_final: 0.7470 (ptt)
REVERT: R  337 MET cc_start: 0.7112 (mmp) cc_final: 0.6907 (mmp)
  outliers start: 25
  outliers final: 18
  residues processed: 205
  average time/residue: 0.0985
  time to fit residues: 27.2352
Evaluate side-chains
  211 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain R residue  103 LYS
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 59 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 110 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 82 optimal weight:   40.0000
   chunk 58 optimal weight:    0.8980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 GLN
R 382 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.103224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.075014 restraints weight = 25000.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.86
r_work: 0.3148 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9300  Z= 0.131
  Angle     :  0.705  15.867  12601  Z= 0.356
  Chirality :  0.044   0.201   1435
  Planarity :  0.004   0.044   1586
  Dihedral  :  4.039  17.873   1258
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.40 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.25), residues: 1143
  helix:  1.76 (0.25), residues: 422
  sheet: -0.08 (0.30), residues: 284
  loop : -0.31 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  32 
 TYR   0.026   0.001   TYR R 366 
 PHE   0.018   0.001   PHE A 259 
 TRP   0.017   0.001   TRP B 187 
 HIS   0.005   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 9296)
  covalent geometry    : angle       0.70400 /  0.36 (12593)
  SS BOND              : bond        0.00303 /  0.15 (    4)
  SS BOND              : angle       1.56324 /  0.93 (    8)
  hydrogen bonds       : bond        0.03615 /  2.40 (  498)
  hydrogen bonds       : angle       4.95914 /  3.48 ( 1410)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 196
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   21 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8322 (ttm-80)
REVERT: A   26 ASP cc_start: 0.8960 (p0) cc_final: 0.8530 (p0)
REVERT: A  252 SER cc_start: 0.9345 (t) cc_final: 0.8976 (p)
REVERT: A  255 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8803 (m-40)
REVERT: A  256 ASN cc_start: 0.8386 (t0) cc_final: 0.7916 (t0)
REVERT: A  281 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (t)
REVERT: A  302 TYR cc_start: 0.9168 (t80) cc_final: 0.8591 (t80)
REVERT: A  306 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8266 (mm-40)
REVERT: A  313 ARG cc_start: 0.8138 (ptp-110) cc_final: 0.7791 (ptp-170)
REVERT: A  317 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8252 (mtmt)
REVERT: A  325 CYS cc_start: 0.8747 (m) cc_final: 0.8136 (p)
REVERT: B   41 LYS cc_start: 0.9619 (tttt) cc_final: 0.9396 (ptpp)
REVERT: B  235 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7407 (ppp)
REVERT: B  244 GLU cc_start: 0.8583 (mp0) cc_final: 0.8016 (mp0)
REVERT: B  280 MET cc_start: 0.8425 (mmm) cc_final: 0.8131 (mmm)
REVERT: B  298 LYS cc_start: 0.9199 (tttp) cc_final: 0.8810 (tttm)
REVERT: C   11 GLN cc_start: 0.9506 (tp40) cc_final: 0.9291 (mp10)
REVERT: C   21 MET cc_start: 0.9255 (tmm) cc_final: 0.8948 (tmm)
REVERT: C   26 ASP cc_start: 0.9533 (m-30) cc_final: 0.9231 (t0)
REVERT: C   42 GLU cc_start: 0.9225 (pp20) cc_final: 0.8925 (pp20)
REVERT: C   46 LYS cc_start: 0.9313 (mmmt) cc_final: 0.8919 (tppt)
REVERT: D   43 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9046 (mmmm)
REVERT: D   73 ASP cc_start: 0.7685 (t0) cc_final: 0.7155 (t0)
REVERT: D   89 GLU cc_start: 0.9079 (pm20) cc_final: 0.8444 (pm20)
REVERT: D   90 ASP cc_start: 0.8841 (m-30) cc_final: 0.7878 (m-30)
REVERT: D   93 MET cc_start: 0.8870 (tpp) cc_final: 0.8656 (tpp)
REVERT: D   94 TYR cc_start: 0.8830 (m-80) cc_final: 0.8262 (m-10)
REVERT: D  186 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7671 (mm110)
REVERT: R   71 ASP cc_start: 0.8738 (p0) cc_final: 0.8468 (p0)
REVERT: R  128 LEU cc_start: 0.9259 (mt) cc_final: 0.8628 (tp)
REVERT: R  129 LEU cc_start: 0.9381 (mt) cc_final: 0.9166 (mm)
REVERT: R  205 TRP cc_start: 0.8157 (m100) cc_final: 0.7598 (t60)
REVERT: R  255 MET cc_start: 0.9227 (mmm) cc_final: 0.8720 (mmm)
REVERT: R  261 MET cc_start: 0.7871 (ptt) cc_final: 0.7594 (ptt)
REVERT: R  337 MET cc_start: 0.7092 (mmp) cc_final: 0.6887 (mmp)
  outliers start: 20
  outliers final: 17
  residues processed: 203
  average time/residue: 0.0984
  time to fit residues: 26.8882
Evaluate side-chains
  207 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  252 PHE
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue  230 MET
Chi-restraints excluded: chain R residue  103 LYS
Chi-restraints excluded: chain R residue  186 PHE
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  256 SER
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  382 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 87 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   overall best weight:    3.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 255 ASN
A 294 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  93 ASN
R 382 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.101509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.073287 restraints weight = 24958.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.77
r_work: 0.3123 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.6047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9300  Z= 0.175
  Angle     :  0.729  15.635  12601  Z= 0.370
  Chirality :  0.045   0.177   1435
  Planarity :  0.004   0.043   1586
  Dihedral  :  4.179  18.422   1258
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.60 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.25), residues: 1143
  helix:  1.74 (0.25), residues: 421
  sheet: -0.18 (0.30), residues: 286
  loop : -0.38 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  32 
 TYR   0.025   0.002   TYR R 366 
 PHE   0.018   0.001   PHE A 259 
 TRP   0.016   0.001   TRP B 100 
 HIS   0.004   0.001   HIS R 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 ( 9296)
  covalent geometry    : angle       0.72798 /  0.37 (12593)
  SS BOND              : bond        0.00251 /  0.12 (    4)
  SS BOND              : angle       1.52138 /  0.91 (    8)
  hydrogen bonds       : bond        0.03744 /  2.49 (  498)
  hydrogen bonds       : angle       5.00401 /  3.51 ( 1410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2425.32 seconds
wall clock time: 42 minutes 21.28 seconds (2541.28 seconds total)