Starting phenix.real_space_refine
on Wed Sep 17 11:52:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d68_30590/09_2025/7d68_30590.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5447      2.51       5
     N    1496      2.21       5
     O    1571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8564
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1885
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 249
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
    Chain: "R"
      Number of atoms: 2426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2426
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 8, 'TRANS': 283}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.04, per 1000 atoms: 0.24
  Number of scatterers: 8564
  At special positions: 0
  Unit cell: (104.442, 95.316, 137.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1571      8.00
     N    1496      7.00
     C    5447      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 260 " - pdb=" SG  CYS R 330 " 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: 0.68
  Conformation dependent library (CDL) restraints added in 545.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      41.1% alpha, 19.3% 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 12 through 38
      removed outlier: 3.978A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.764A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.792A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.922A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.753A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.685A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.990A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.616A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.718A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.533A  pdb=" N   PHE P   6 " --> pdb=" O   ALA P   2 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 203
      removed outlier: 3.844A  pdb=" N   ASP R 170 " --> pdb=" O   LYS R 166 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU R 174 " --> pdb=" O   ASP R 170 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU R 199 " --> pdb=" O   LEU R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 239
    Processing helix  chain 'R' and resid 252 through 257
      removed outlier: 3.567A  pdb=" N   GLU R 255 " --> pdb=" O   TYR R 252 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   MET R 256 " --> pdb=" O   LEU R 253 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   SER R 257 " --> pdb=" O   SER R 254 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 252 through 257'
    Processing helix  chain 'R' and resid 258 through 288
      removed outlier: 3.697A  pdb=" N   SER R 262 " --> pdb=" O   THR R 258 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 308
    Processing helix  chain 'R' and resid 311 through 325
      Proline residue:  R 317  - end of helix
      removed outlier: 3.855A  pdb=" N   ALA R 323 " --> pdb=" O   GLY R 319 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 340 through 371
      Proline residue:  R 346  - end of helix
      removed outlier: 4.074A  pdb=" N   CYS R 350 " --> pdb=" O   PRO R 346 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN R 354 " --> pdb=" O   CYS R 350 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA R 371 " --> pdb=" O   SER R 367 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 375 through 395
      Proline residue:  R 392  - end of helix
    Processing helix  chain 'R' and resid 398 through 404
      removed outlier: 3.557A  pdb=" N   PHE R 403 " --> pdb=" O   ILE R 399 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE R 404 " --> pdb=" O   LEU R 400 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 411 through 437
      removed outlier: 3.559A  pdb=" N   LEU R 415 " --> pdb=" O   GLY R 411 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLY R 429 " --> pdb=" O   SER R 425 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   PHE R 430 " --> pdb=" O   SER R 426 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 440 through 452
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.608A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.592A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.901A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.989A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.638A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.939A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.483A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.684A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.516A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 5.616A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1152 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: 1.01

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2187
        1.33 -     1.45: 1828
        1.45 -     1.58: 4652
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 8739
  Sorted by residual:
  bond pdb=" C   ARG R 210 "
       pdb=" O   ARG R 210 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.48e+00
  bond pdb=" C   LEU R 206 "
       pdb=" O   LEU R 206 "
    ideal  model  delta    sigma   weight residual
    1.236  1.209  0.027 1.32e-02 5.74e+03 4.11e+00
  bond pdb=" CA  ALA A 226 "
       pdb=" C   ALA A 226 "
    ideal  model  delta    sigma   weight residual
    1.531  1.514  0.017 1.12e-02 7.97e+03 2.35e+00
  bond pdb=" C   TYR A 358 "
       pdb=" O   TYR A 358 "
    ideal  model  delta    sigma   weight residual
    1.234  1.215  0.018 1.22e-02 6.72e+03 2.29e+00
  bond pdb=" C   HIS A 357 "
       pdb=" O   HIS A 357 "
    ideal  model  delta    sigma   weight residual
    1.234  1.216  0.017 1.24e-02 6.50e+03 1.99e+00
  ... (remaining 8734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 11632
        2.12 -     4.24: 169
        4.24 -     6.36: 18
        6.36 -     8.48: 5
        8.48 -    10.60: 1
  Bond angle restraints: 11825
  Sorted by residual:
  angle pdb=" N   ARG A 356 "
        pdb=" CA  ARG A 356 "
        pdb=" C   ARG A 356 "
      ideal   model   delta    sigma   weight residual
     113.88  105.69    8.19 1.23e+00 6.61e-01 4.43e+01
  angle pdb=" N   HIS R 207 "
        pdb=" CA  HIS R 207 "
        pdb=" C   HIS R 207 "
      ideal   model   delta    sigma   weight residual
     110.80  121.40  -10.60 2.13e+00 2.20e-01 2.48e+01
  angle pdb=" N   GLU A 309 "
        pdb=" CA  GLU A 309 "
        pdb=" C   GLU A 309 "
      ideal   model   delta    sigma   weight residual
     112.04  106.17    5.87 1.44e+00 4.82e-01 1.66e+01
  angle pdb=" N   GLU R 442 "
        pdb=" CA  GLU R 442 "
        pdb=" C   GLU R 442 "
      ideal   model   delta    sigma   weight residual
     111.28  115.36   -4.08 1.09e+00 8.42e-01 1.40e+01
  angle pdb=" N   SER R 402 "
        pdb=" CA  SER R 402 "
        pdb=" C   SER R 402 "
      ideal   model   delta    sigma   weight residual
     111.28  107.40    3.88 1.09e+00 8.42e-01 1.27e+01
  ... (remaining 11820 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 4680
       16.16 -    32.32: 401
       32.32 -    48.48: 84
       48.48 -    64.64: 17
       64.64 -    80.80: 6
  Dihedral angle restraints: 5188
    sinusoidal: 2077
      harmonic: 3111
  Sorted by residual:
  dihedral pdb=" CB  CYS R 260 "
           pdb=" SG  CYS R 260 "
           pdb=" SG  CYS R 330 "
           pdb=" CB  CYS R 330 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.15   52.85     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.23  -21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  LYS A 216 "
           pdb=" C   LYS A 216 "
           pdb=" N   VAL A 217 "
           pdb=" CA  VAL A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 5185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1205
       0.080 -    0.159: 109
       0.159 -    0.239: 2
       0.239 -    0.318: 0
       0.318 -    0.398: 1
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  HIS R 207 "
            pdb=" N   HIS R 207 "
            pdb=" C   HIS R 207 "
            pdb=" CB  HIS R 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.96e+00
  chirality pdb=" CA  ASP A 354 "
            pdb=" N   ASP A 354 "
            pdb=" C   ASP A 354 "
            pdb=" CB  ASP A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  ILE R 404 "
            pdb=" N   ILE R 404 "
            pdb=" C   ILE R 404 "
            pdb=" CB  ILE R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 345 "    0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO R 346 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO R 346 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 346 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.014 2.00e-02 2.50e+03   1.37e-02 3.74e+00
        pdb=" CG  TYR B  59 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 350 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   THR A 350 "    0.029 2.00e-02 2.50e+03
        pdb=" O   THR A 350 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 351 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1500 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 137
        2.68 -     3.23: 8179
        3.23 -     3.79: 12857
        3.79 -     4.34: 17957
        4.34 -     4.90: 30124
  Nonbonded interactions: 69254
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" OG1 THR A 364 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" NH1 ARG B  22 "
            pdb=" O   ALA B 257 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" ND2 ASN N  35 "
            pdb=" OD2 ASP N 109 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OE1 GLU R 281 "
            pdb=" O   HOH R 701 "
     model   vdw
     2.244 3.040
  ... (remaining 69249 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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.500
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8741  Z= 0.193
  Angle     :  0.664  10.598  11829  Z= 0.395
  Chirality :  0.045   0.398   1317
  Planarity :  0.004   0.050   1503
  Dihedral  : 13.068  80.805   3170
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  3.89 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.23), residues: 1052
  helix: -0.47 (0.23), residues: 390
  sheet: -1.37 (0.32), residues: 220
  loop : -2.17 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  22 
 TYR   0.034   0.002   TYR B  59 
 PHE   0.015   0.002   PHE A 222 
 TRP   0.018   0.002   TRP B  99 
 HIS   0.007   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8739)
  covalent geometry    : angle       0.66377 (11825)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       1.64694 (    4)
  hydrogen bonds       : bond        0.16442 (  400)
  hydrogen bonds       : angle       6.35834 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6675 (tm-30)
REVERT: A  341 ILE cc_start: 0.7881 (mm) cc_final: 0.7526 (mm)
REVERT: A  373 ARG cc_start: 0.7304 (mmm160) cc_final: 0.7072 (mmt180)
REVERT: R  215 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7586 (mtp)
REVERT: R  338 LYS cc_start: 0.7552 (mttm) cc_final: 0.6846 (tttp)
  outliers start: 7
  outliers final: 2
  residues processed: 157
  average time/residue: 0.6386
  time to fit residues: 105.8238
Evaluate side-chains
  124 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain P residue    1 HIS
Chi-restraints excluded: chain R residue  215 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
A 371 ASN
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
N  77 ASN
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 372 HIS
R 408 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.188799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149130 restraints weight = 9701.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.19
r_work: 0.3464 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8741  Z= 0.171
  Angle     :  0.619   7.907  11829  Z= 0.325
  Chirality :  0.043   0.165   1317
  Planarity :  0.004   0.053   1503
  Dihedral  :  5.002  31.010   1176
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.53 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.25), residues: 1052
  helix:  0.64 (0.25), residues: 412
  sheet: -0.82 (0.33), residues: 212
  loop : -1.84 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  22 
 TYR   0.029   0.002   TYR R 182 
 PHE   0.020   0.002   PHE R 202 
 TRP   0.016   0.002   TRP B  99 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8739)
  covalent geometry    : angle       0.61892 (11825)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       1.42228 (    4)
  hydrogen bonds       : bond        0.05173 (  400)
  hydrogen bonds       : angle       4.84454 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   12 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6431 (tm-30)
REVERT: A  268 GLU cc_start: 0.7653 (mp0) cc_final: 0.7286 (mp0)
REVERT: A  341 ILE cc_start: 0.7801 (mm) cc_final: 0.7570 (mm)
REVERT: B  145 TYR cc_start: 0.9102 (p90) cc_final: 0.8888 (p90)
REVERT: B  270 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7627 (pp)
REVERT: B  290 ASP cc_start: 0.7808 (m-30) cc_final: 0.7481 (m-30)
REVERT: N   80 TYR cc_start: 0.7727 (m-10) cc_final: 0.7458 (m-80)
REVERT: N   83 MET cc_start: 0.6882 (mtm) cc_final: 0.6526 (mtp)
REVERT: R  255 GLU cc_start: 0.7140 (mp0) cc_final: 0.6882 (mp0)
REVERT: R  326 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.5609 (mp0)
REVERT: R  338 LYS cc_start: 0.7770 (mttm) cc_final: 0.6728 (tttp)
  outliers start: 16
  outliers final: 4
  residues processed: 131
  average time/residue: 0.6412
  time to fit residues: 89.0371
Evaluate side-chains
  124 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  326 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 84 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 94 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A  35 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.188328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.148310 restraints weight = 9447.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.16
r_work: 0.3486 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8741  Z= 0.162
  Angle     :  0.588   7.044  11829  Z= 0.310
  Chirality :  0.043   0.165   1317
  Planarity :  0.004   0.058   1503
  Dihedral  :  4.631  21.615   1170
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.77 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.25), residues: 1052
  helix:  1.02 (0.25), residues: 412
  sheet: -0.65 (0.33), residues: 212
  loop : -1.71 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 344 
 TYR   0.026   0.001   TYR R 182 
 PHE   0.021   0.002   PHE R 202 
 TRP   0.016   0.002   TRP B  99 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8739)
  covalent geometry    : angle       0.58770 (11825)
  SS BOND              : bond        0.00330 (    2)
  SS BOND              : angle       1.11056 (    4)
  hydrogen bonds       : bond        0.04867 (  400)
  hydrogen bonds       : angle       4.57608 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7904 (pttm)
REVERT: A  268 GLU cc_start: 0.7694 (mp0) cc_final: 0.7253 (mp0)
REVERT: A  341 ILE cc_start: 0.7845 (mm) cc_final: 0.7612 (mm)
REVERT: B   59 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8411 (m-80)
REVERT: B  145 TYR cc_start: 0.9108 (p90) cc_final: 0.8887 (p90)
REVERT: B  198 LEU cc_start: 0.8938 (mt) cc_final: 0.8703 (mt)
REVERT: B  262 MET cc_start: 0.7813 (mpp) cc_final: 0.7340 (mpt)
REVERT: B  270 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7685 (pp)
REVERT: B  290 ASP cc_start: 0.7804 (m-30) cc_final: 0.7476 (m-30)
REVERT: N   80 TYR cc_start: 0.7688 (m-10) cc_final: 0.7422 (m-80)
REVERT: N   83 MET cc_start: 0.6867 (mtm) cc_final: 0.6584 (mtp)
REVERT: R  326 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5668 (mp0)
REVERT: R  338 LYS cc_start: 0.7804 (mttm) cc_final: 0.6766 (tttp)
REVERT: R  412 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5100 (t80)
  outliers start: 20
  outliers final: 5
  residues processed: 126
  average time/residue: 0.6066
  time to fit residues: 81.3717
Evaluate side-chains
  129 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  412 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.187200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.146616 restraints weight = 9744.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.22
r_work: 0.3465 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8741  Z= 0.177
  Angle     :  0.594   8.874  11829  Z= 0.310
  Chirality :  0.043   0.158   1317
  Planarity :  0.004   0.059   1503
  Dihedral  :  4.596  22.000   1170
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.85 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.25), residues: 1052
  helix:  1.15 (0.26), residues: 412
  sheet: -0.64 (0.33), residues: 211
  loop : -1.64 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 344 
 TYR   0.026   0.001   TYR R 182 
 PHE   0.024   0.002   PHE R 202 
 TRP   0.017   0.002   TRP B  99 
 HIS   0.005   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8739)
  covalent geometry    : angle       0.59399 (11825)
  SS BOND              : bond        0.00313 (    2)
  SS BOND              : angle       1.17151 (    4)
  hydrogen bonds       : bond        0.04845 (  400)
  hydrogen bonds       : angle       4.48279 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7779 (pttm)
REVERT: A  341 ILE cc_start: 0.7842 (mm) cc_final: 0.7540 (mm)
REVERT: B   59 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8613 (m-80)
REVERT: B   61 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8738 (ppp)
REVERT: B  198 LEU cc_start: 0.8910 (mt) cc_final: 0.8687 (mt)
REVERT: B  270 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7765 (pp)
REVERT: B  290 ASP cc_start: 0.7801 (m-30) cc_final: 0.7485 (m-30)
REVERT: N   68 PHE cc_start: 0.7061 (m-10) cc_final: 0.6827 (m-10)
REVERT: N   80 TYR cc_start: 0.7743 (m-10) cc_final: 0.7463 (m-80)
REVERT: R  255 GLU cc_start: 0.7122 (mp0) cc_final: 0.6833 (mp0)
REVERT: R  302 ARG cc_start: 0.6884 (mtp180) cc_final: 0.6125 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.5712 (mp0)
REVERT: R  338 LYS cc_start: 0.7892 (mttm) cc_final: 0.6789 (tttp)
REVERT: R  398 GLU cc_start: 0.7701 (mp0) cc_final: 0.7470 (mp0)
REVERT: R  412 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5027 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 130
  average time/residue: 0.6167
  time to fit residues: 85.3543
Evaluate side-chains
  136 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  412 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0670
   chunk 78 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.189751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149623 restraints weight = 9564.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.20
r_work: 0.3503 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8741  Z= 0.116
  Angle     :  0.526   7.948  11829  Z= 0.277
  Chirality :  0.040   0.150   1317
  Planarity :  0.004   0.061   1503
  Dihedral  :  4.323  20.670   1170
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.95 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.26), residues: 1052
  helix:  1.41 (0.26), residues: 419
  sheet: -0.53 (0.33), residues: 211
  loop : -1.52 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 344 
 TYR   0.022   0.001   TYR R 182 
 PHE   0.024   0.001   PHE R 202 
 TRP   0.014   0.001   TRP B  99 
 HIS   0.002   0.001   HIS P   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8739)
  covalent geometry    : angle       0.52562 (11825)
  SS BOND              : bond        0.00288 (    2)
  SS BOND              : angle       0.82249 (    4)
  hydrogen bonds       : bond        0.04203 (  400)
  hydrogen bonds       : angle       4.20981 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (pttm)
REVERT: A  268 GLU cc_start: 0.7664 (mp0) cc_final: 0.6964 (mp0)
REVERT: A  280 ARG cc_start: 0.8295 (tpt90) cc_final: 0.7904 (tpt90)
REVERT: A  341 ILE cc_start: 0.7739 (mm) cc_final: 0.7487 (mm)
REVERT: B   59 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8538 (m-80)
REVERT: B   61 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8660 (ppp)
REVERT: B  262 MET cc_start: 0.7831 (mpp) cc_final: 0.7612 (mpt)
REVERT: B  270 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7819 (pp)
REVERT: B  290 ASP cc_start: 0.7682 (m-30) cc_final: 0.7399 (m-30)
REVERT: N   20 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7381 (mm)
REVERT: N   68 PHE cc_start: 0.6981 (m-10) cc_final: 0.6756 (m-10)
REVERT: N   80 TYR cc_start: 0.7483 (m-10) cc_final: 0.7210 (m-80)
REVERT: R  255 GLU cc_start: 0.7124 (mp0) cc_final: 0.6916 (mp0)
REVERT: R  302 ARG cc_start: 0.6798 (mtp180) cc_final: 0.6027 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5673 (mp0)
REVERT: R  338 LYS cc_start: 0.7860 (mttm) cc_final: 0.6743 (tttp)
REVERT: R  412 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.4766 (t80)
  outliers start: 31
  outliers final: 17
  residues processed: 134
  average time/residue: 0.6029
  time to fit residues: 86.0926
Evaluate side-chains
  139 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  412 PHE
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.192075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151732 restraints weight = 9603.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.24
r_work: 0.3555 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8741  Z= 0.115
  Angle     :  0.518   7.317  11829  Z= 0.272
  Chirality :  0.040   0.150   1317
  Planarity :  0.004   0.059   1503
  Dihedral  :  4.188  20.108   1170
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.47 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.26), residues: 1052
  helix:  1.59 (0.26), residues: 415
  sheet: -0.21 (0.35), residues: 203
  loop : -1.47 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 344 
 TYR   0.021   0.001   TYR R 182 
 PHE   0.026   0.001   PHE R 202 
 TRP   0.014   0.001   TRP B  99 
 HIS   0.002   0.001   HIS R 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8739)
  covalent geometry    : angle       0.51790 (11825)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.84859 (    4)
  hydrogen bonds       : bond        0.04058 (  400)
  hydrogen bonds       : angle       4.08433 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   41 HIS cc_start: 0.8545 (m170) cc_final: 0.8298 (m90)
REVERT: A  211 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7800 (pttm)
REVERT: A  268 GLU cc_start: 0.7651 (mp0) cc_final: 0.7347 (mm-30)
REVERT: A  341 ILE cc_start: 0.7812 (mm) cc_final: 0.7552 (mm)
REVERT: B   59 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8577 (m-80)
REVERT: B   61 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8641 (ppp)
REVERT: B  134 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.6974 (ptp-170)
REVERT: B  145 TYR cc_start: 0.9158 (p90) cc_final: 0.8946 (p90)
REVERT: B  262 MET cc_start: 0.7823 (mpp) cc_final: 0.7593 (mpt)
REVERT: B  270 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7708 (pp)
REVERT: B  290 ASP cc_start: 0.7731 (m-30) cc_final: 0.7458 (m-30)
REVERT: N   20 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7480 (mm)
REVERT: N   68 PHE cc_start: 0.6821 (m-10) cc_final: 0.6516 (m-80)
REVERT: N   80 TYR cc_start: 0.7438 (m-10) cc_final: 0.7161 (m-80)
REVERT: R  188 PHE cc_start: 0.7527 (m-10) cc_final: 0.6969 (t80)
REVERT: R  255 GLU cc_start: 0.7187 (mp0) cc_final: 0.6978 (mp0)
REVERT: R  302 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6124 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.5674 (mp0)
REVERT: R  338 LYS cc_start: 0.7911 (mttm) cc_final: 0.6833 (tttp)
  outliers start: 30
  outliers final: 16
  residues processed: 132
  average time/residue: 0.5794
  time to fit residues: 81.4392
Evaluate side-chains
  138 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain P residue   23 ILE
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  362 LEU
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 89 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  28 GLN
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.189500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.148712 restraints weight = 9863.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.27
r_work: 0.3553 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8741  Z= 0.118
  Angle     :  0.518   7.119  11829  Z= 0.272
  Chirality :  0.040   0.150   1317
  Planarity :  0.004   0.059   1503
  Dihedral  :  4.118  19.546   1170
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.03 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.26), residues: 1052
  helix:  1.74 (0.26), residues: 409
  sheet:  0.08 (0.36), residues: 192
  loop : -1.49 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 344 
 TYR   0.021   0.001   TYR R 182 
 PHE   0.026   0.001   PHE R 202 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.002   0.001   HIS R 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8739)
  covalent geometry    : angle       0.51786 (11825)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       0.82457 (    4)
  hydrogen bonds       : bond        0.04037 (  400)
  hydrogen bonds       : angle       4.04119 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 118
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7805 (pttm)
REVERT: A  268 GLU cc_start: 0.7663 (mp0) cc_final: 0.7370 (mm-30)
REVERT: A  341 ILE cc_start: 0.7822 (mm) cc_final: 0.7533 (mm)
REVERT: B   59 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8619 (m-80)
REVERT: B   61 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8653 (ppp)
REVERT: B  134 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.6963 (ptp-170)
REVERT: B  145 TYR cc_start: 0.9164 (p90) cc_final: 0.8923 (p90)
REVERT: B  270 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7732 (pp)
REVERT: B  290 ASP cc_start: 0.7720 (m-30) cc_final: 0.7420 (m-30)
REVERT: G   47 GLU cc_start: 0.6509 (mp0) cc_final: 0.5448 (mp0)
REVERT: N   68 PHE cc_start: 0.6772 (m-10) cc_final: 0.6561 (m-80)
REVERT: N   80 TYR cc_start: 0.7417 (m-10) cc_final: 0.7122 (m-80)
REVERT: R  188 PHE cc_start: 0.7524 (m-10) cc_final: 0.6972 (t80)
REVERT: R  255 GLU cc_start: 0.7160 (mp0) cc_final: 0.6838 (mp0)
REVERT: R  302 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6232 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5697 (mp0)
REVERT: R  338 LYS cc_start: 0.7913 (mttm) cc_final: 0.6868 (tttp)
  outliers start: 37
  outliers final: 21
  residues processed: 139
  average time/residue: 0.5629
  time to fit residues: 83.8076
Evaluate side-chains
  141 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  362 LEU
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 80 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    0.1980
   chunk 6 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0370
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.191137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150527 restraints weight = 9686.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.26
r_work: 0.3570 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8741  Z= 0.108
  Angle     :  0.520   6.764  11829  Z= 0.272
  Chirality :  0.040   0.148   1317
  Planarity :  0.004   0.058   1503
  Dihedral  :  4.024  18.925   1170
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.57 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.26), residues: 1052
  helix:  1.83 (0.26), residues: 410
  sheet:  0.18 (0.36), residues: 191
  loop : -1.46 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 344 
 TYR   0.019   0.001   TYR R 182 
 PHE   0.026   0.001   PHE R 202 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.002   0.000   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8739)
  covalent geometry    : angle       0.51966 (11825)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.98737 (    4)
  hydrogen bonds       : bond        0.03844 (  400)
  hydrogen bonds       : angle       3.95627 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7780 (pttm)
REVERT: A  268 GLU cc_start: 0.7667 (mp0) cc_final: 0.7329 (mm-30)
REVERT: A  341 ILE cc_start: 0.7798 (mm) cc_final: 0.7537 (mm)
REVERT: B   59 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8569 (m-80)
REVERT: B   61 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8547 (pp-130)
REVERT: B  134 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.6912 (ptp-170)
REVERT: B  145 TYR cc_start: 0.9129 (p90) cc_final: 0.8872 (p90)
REVERT: B  270 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7704 (pp)
REVERT: B  290 ASP cc_start: 0.7701 (m-30) cc_final: 0.7419 (m-30)
REVERT: N   80 TYR cc_start: 0.7296 (m-10) cc_final: 0.7021 (m-80)
REVERT: R  188 PHE cc_start: 0.7502 (m-10) cc_final: 0.6956 (t80)
REVERT: R  255 GLU cc_start: 0.7235 (mp0) cc_final: 0.7011 (mp0)
REVERT: R  256 MET cc_start: 0.4426 (mmt) cc_final: 0.4045 (ptp)
REVERT: R  302 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6167 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5678 (mp0)
REVERT: R  338 LYS cc_start: 0.7914 (mttm) cc_final: 0.6878 (tttp)
  outliers start: 33
  outliers final: 18
  residues processed: 137
  average time/residue: 0.5814
  time to fit residues: 85.1668
Evaluate side-chains
  137 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue  106 ASP
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  362 LEU
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  28 GLN
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.190743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150115 restraints weight = 9727.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.25
r_work: 0.3613 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8741  Z= 0.119
  Angle     :  0.531   8.093  11829  Z= 0.278
  Chirality :  0.041   0.149   1317
  Planarity :  0.004   0.058   1503
  Dihedral  :  4.046  18.241   1170
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.90 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1052
  helix:  1.71 (0.26), residues: 416
  sheet:  0.17 (0.36), residues: 191
  loop : -1.41 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 344 
 TYR   0.021   0.001   TYR R 182 
 PHE   0.046   0.002   PHE N  68 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8739)
  covalent geometry    : angle       0.53032 (11825)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.99751 (    4)
  hydrogen bonds       : bond        0.03941 (  400)
  hydrogen bonds       : angle       3.97133 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (pttm)
REVERT: A  220 HIS cc_start: 0.8017 (m-70) cc_final: 0.7771 (t-90)
REVERT: A  268 GLU cc_start: 0.7645 (mp0) cc_final: 0.7346 (mm-30)
REVERT: A  341 ILE cc_start: 0.7859 (mm) cc_final: 0.7555 (mm)
REVERT: B   59 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8614 (m-80)
REVERT: B   61 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8542 (pp-130)
REVERT: B  134 ARG cc_start: 0.7407 (ptp-110) cc_final: 0.6984 (ptp-170)
REVERT: B  145 TYR cc_start: 0.9142 (p90) cc_final: 0.8889 (p90)
REVERT: B  270 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7880 (pp)
REVERT: B  290 ASP cc_start: 0.7705 (m-30) cc_final: 0.7453 (m-30)
REVERT: N   83 MET cc_start: 0.6815 (mtm) cc_final: 0.6523 (mtp)
REVERT: R  188 PHE cc_start: 0.7575 (m-10) cc_final: 0.7033 (t80)
REVERT: R  255 GLU cc_start: 0.7313 (mp0) cc_final: 0.7036 (mp0)
REVERT: R  256 MET cc_start: 0.4557 (mmt) cc_final: 0.4137 (ptp)
REVERT: R  302 ARG cc_start: 0.6917 (mtp180) cc_final: 0.6245 (mmt-90)
REVERT: R  326 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5721 (mp0)
REVERT: R  338 LYS cc_start: 0.7964 (mttm) cc_final: 0.6960 (tttp)
  outliers start: 29
  outliers final: 17
  residues processed: 132
  average time/residue: 0.5845
  time to fit residues: 82.3650
Evaluate side-chains
  134 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  362 LEU
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0770
   chunk 93 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    0.3980
   chunk 95 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 239 ASN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.193471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153964 restraints weight = 9617.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.21
r_work: 0.3630 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8741  Z= 0.110
  Angle     :  0.524   9.324  11829  Z= 0.274
  Chirality :  0.040   0.146   1317
  Planarity :  0.004   0.058   1503
  Dihedral  :  4.013  23.138   1170
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.65 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1052
  helix:  1.79 (0.26), residues: 416
  sheet:  0.20 (0.36), residues: 191
  loop : -1.35 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 344 
 TYR   0.019   0.001   TYR R 182 
 PHE   0.038   0.001   PHE N  68 
 TRP   0.013   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8739)
  covalent geometry    : angle       0.52346 (11825)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.91513 (    4)
  hydrogen bonds       : bond        0.03801 (  400)
  hydrogen bonds       : angle       3.91771 ( 1152)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7715 (pttm)
REVERT: A  220 HIS cc_start: 0.8020 (m-70) cc_final: 0.7714 (t-90)
REVERT: A  268 GLU cc_start: 0.7590 (mp0) cc_final: 0.7345 (mm-30)
REVERT: A  341 ILE cc_start: 0.7828 (mm) cc_final: 0.7524 (mm)
REVERT: B   59 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (m-80)
REVERT: B   61 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8534 (pp-130)
REVERT: B  134 ARG cc_start: 0.7391 (ptp-110) cc_final: 0.6984 (ptp-170)
REVERT: B  145 TYR cc_start: 0.9131 (p90) cc_final: 0.8889 (p90)
REVERT: B  270 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7914 (pp)
REVERT: B  290 ASP cc_start: 0.7740 (m-30) cc_final: 0.7476 (m-30)
REVERT: N   80 TYR cc_start: 0.7516 (m-80) cc_final: 0.7118 (m-80)
REVERT: N   83 MET cc_start: 0.6759 (mtm) cc_final: 0.6457 (mtp)
REVERT: R  188 PHE cc_start: 0.7550 (m-10) cc_final: 0.7006 (t80)
REVERT: R  255 GLU cc_start: 0.7410 (mp0) cc_final: 0.7168 (mp0)
REVERT: R  256 MET cc_start: 0.4630 (mmt) cc_final: 0.4203 (ptp)
REVERT: R  302 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6649 (mtp-110)
REVERT: R  326 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.5669 (mp0)
REVERT: R  338 LYS cc_start: 0.7935 (mttm) cc_final: 0.6948 (tttp)
  outliers start: 25
  outliers final: 14
  residues processed: 129
  average time/residue: 0.6060
  time to fit residues: 83.2590
Evaluate side-chains
  131 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain R residue  182 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  260 CYS
Chi-restraints excluded: chain R residue  326 GLU
Chi-restraints excluded: chain R residue  362 LEU
Chi-restraints excluded: chain R residue  452 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** P   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.192398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152727 restraints weight = 9597.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.21
r_work: 0.3590 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8741  Z= 0.118
  Angle     :  0.527   9.380  11829  Z= 0.275
  Chirality :  0.040   0.146   1317
  Planarity :  0.004   0.058   1503
  Dihedral  :  4.028  22.874   1170
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.22 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 1052
  helix:  1.78 (0.26), residues: 415
  sheet:  0.22 (0.36), residues: 191
  loop : -1.35 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 344 
 TYR   0.020   0.001   TYR R 182 
 PHE   0.035   0.002   PHE N  68 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8739)
  covalent geometry    : angle       0.52639 (11825)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.97671 (    4)
  hydrogen bonds       : bond        0.03906 (  400)
  hydrogen bonds       : angle       3.93670 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3614.35 seconds
wall clock time: 62 minutes 16.24 seconds (3736.24 seconds total)