Starting phenix.real_space_refine
on Tue Mar  3 22:06:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7c2e_30274/03_2026/7c2e_30274_neut.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5632      2.51       5
     N    1529      2.21       5
     O    1613      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8828
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1637
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 6, 'TRANS': 186}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          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: "R"
      Number of atoms: 3152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3152
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 14, 'TRANS': 365}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 41
          Unusual residues: {'FFR': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA R 209 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA R 209 " occ=0.00
  Time building chain proxies: 2.23, per 1000 atoms: 0.25
  Number of scatterers: 8828
  At special positions: 0
  Unit cell: (82.555, 154.66, 121.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     F       1      9.00
     O    1613      8.00
     N    1529      7.00
     C    5632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " 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: 0.78
  Conformation dependent library (CDL) restraints added in 290.2 milliseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      39.7% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 4.000A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 238
      removed outlier: 3.831A  pdb=" N   LYS A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.506A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 318'
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.622A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.626A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'R' and resid 31 through 52
    Processing helix  chain 'R' and resid 138 through 169
    Processing helix  chain 'R' and resid 174 through 198
    Processing helix  chain 'R' and resid 206 through 211
      removed outlier: 3.947A  pdb=" N   GLN R 210 " --> pdb=" O   SER R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 211 through 222
      removed outlier: 3.569A  pdb=" N   ASP R 215 " --> pdb=" O   GLN R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 256
    Processing helix  chain 'R' and resid 261 through 274
    Processing helix  chain 'R' and resid 275 through 292
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 303 through 337
      removed outlier: 4.311A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 360
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 369
    Processing helix  chain 'R' and resid 380 through 391
      removed outlier: 4.279A  pdb=" N   GLU R 387 " --> pdb=" O   LYS R 383 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 405
    Processing helix  chain 'R' and resid 406 through 423
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.707A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.819A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 3.755A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.602A  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: 3.582A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.521A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 150 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.973A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.394A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.383A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5
      removed outlier: 3.750A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.142A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 83 through 84
      removed outlier: 3.617A  pdb=" N   VAL R  83 " --> pdb=" O   VAL R 100 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1170 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: 1.44

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1426
        1.29 -     1.43: 2516
        1.43 -     1.57: 5024
        1.57 -     1.70: 0
        1.70 -     1.84: 71
  Bond restraints: 9037
  Sorted by residual:
  bond pdb=" C21 FFR R 501 "
       pdb=" N20 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.306  1.364 -0.058 2.00e-02 2.50e+03 8.43e+00
  bond pdb=" C36 FFR R 501 "
       pdb=" O39 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.433  1.489 -0.056 2.00e-02 2.50e+03 7.88e+00
  bond pdb=" C38 FFR R 501 "
       pdb=" O39 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.436  1.490 -0.054 2.00e-02 2.50e+03 7.16e+00
  bond pdb=" C   LEU R 118 "
       pdb=" N   PRO R 119 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.028 1.20e-02 6.94e+03 5.49e+00
  bond pdb=" C21 FFR R 501 "
       pdb=" O22 FFR R 501 "
    ideal  model  delta    sigma   weight residual
    1.341  1.382 -0.041 2.00e-02 2.50e+03 4.14e+00
  ... (remaining 9032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11890
        1.92 -     3.83: 288
        3.83 -     5.75: 47
        5.75 -     7.66: 16
        7.66 -     9.58: 11
  Bond angle restraints: 12252
  Sorted by residual:
  angle pdb=" C   ASN R 302 "
        pdb=" N   MET R 303 "
        pdb=" CA  MET R 303 "
      ideal   model   delta    sigma   weight residual
     121.54  131.12   -9.58 1.91e+00 2.74e-01 2.52e+01
  angle pdb=" N   GLY R 361 "
        pdb=" CA  GLY R 361 "
        pdb=" C   GLY R 361 "
      ideal   model   delta    sigma   weight residual
     111.03  117.91   -6.88 1.40e+00 5.10e-01 2.42e+01
  angle pdb=" CA  TYR R 148 "
        pdb=" CB  TYR R 148 "
        pdb=" CG  TYR R 148 "
      ideal   model   delta    sigma   weight residual
     113.90  122.47   -8.57 1.80e+00 3.09e-01 2.27e+01
  angle pdb=" C   LYS N  76 "
        pdb=" N   ASN N  77 "
        pdb=" CA  ASN N  77 "
      ideal   model   delta    sigma   weight residual
     121.54  130.57   -9.03 1.91e+00 2.74e-01 2.23e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.84e+01
  ... (remaining 12247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.00: 5079
       15.00 -    30.00: 189
       30.00 -    45.00: 59
       45.00 -    60.00: 6
       60.00 -    75.00: 3
  Dihedral angle restraints: 5336
    sinusoidal: 2146
      harmonic: 3190
  Sorted by residual:
  dihedral pdb=" CA  SER R 261 "
           pdb=" C   SER R 261 "
           pdb=" N   GLU R 262 "
           pdb=" CA  GLU R 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.27  -28.73     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  ARG R 299 "
           pdb=" C   ARG R 299 "
           pdb=" N   ASN R 300 "
           pdb=" CA  ASN R 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.99  -27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  ARG A 228 "
           pdb=" C   ARG A 228 "
           pdb=" N   ASP A 229 "
           pdb=" CA  ASP A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 932
       0.044 -    0.089: 296
       0.089 -    0.133: 92
       0.133 -    0.177: 15
       0.177 -    0.222: 3
  Chirality restraints: 1338
  Sorted by residual:
  chirality pdb=" CB  THR R 378 "
            pdb=" CA  THR R 378 "
            pdb=" OG1 THR R 378 "
            pdb=" CG2 THR R 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ASN N  77 "
            pdb=" N   ASN N  77 "
            pdb=" C   ASN N  77 "
            pdb=" CB  ASN N  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.33e-01
  ... (remaining 1335 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 FFR R 501 "   -0.146 2.00e-02 2.50e+03   8.09e-02 1.96e+02
        pdb=" C04 FFR R 501 "   -0.018 2.00e-02 2.50e+03
        pdb=" C06 FFR R 501 "    0.033 2.00e-02 2.50e+03
        pdb=" C07 FFR R 501 "    0.038 2.00e-02 2.50e+03
        pdb=" C08 FFR R 501 "    0.060 2.00e-02 2.50e+03
        pdb=" C09 FFR R 501 "    0.040 2.00e-02 2.50e+03
        pdb=" C11 FFR R 501 "   -0.025 2.00e-02 2.50e+03
        pdb=" C12 FFR R 501 "   -0.177 2.00e-02 2.50e+03
        pdb=" C35 FFR R 501 "    0.120 2.00e-02 2.50e+03
        pdb=" N1  FFR R 501 "    0.010 2.00e-02 2.50e+03
        pdb=" N10 FFR R 501 "    0.014 2.00e-02 2.50e+03
        pdb=" N34 FFR R 501 "    0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  FFR R 501 "   -0.020 2.00e-02 2.50e+03   5.18e-02 6.72e+01
        pdb=" C23 FFR R 501 "   -0.118 2.00e-02 2.50e+03
        pdb=" C24 FFR R 501 "    0.011 2.00e-02 2.50e+03
        pdb=" C25 FFR R 501 "    0.042 2.00e-02 2.50e+03
        pdb=" C26 FFR R 501 "    0.052 2.00e-02 2.50e+03
        pdb=" C28 FFR R 501 "    0.030 2.00e-02 2.50e+03
        pdb=" C29 FFR R 501 "    0.025 2.00e-02 2.50e+03
        pdb=" C30 FFR R 501 "    0.027 2.00e-02 2.50e+03
        pdb=" F1  FFR R 501 "    0.022 2.00e-02 2.50e+03
        pdb=" N2  FFR R 501 "   -0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 303 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   MET R 303 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   MET R 303 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN R 304 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 91
        2.64 -     3.20: 7226
        3.20 -     3.77: 13439
        3.77 -     4.33: 17709
        4.33 -     4.90: 29444
  Nonbonded interactions: 67909
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" ND1 HIS G  44 "
            pdb=" OE2 GLU G  47 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OD2 ASP R  67 "
            pdb=" NH2 ARG R 102 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" NZ  LYS A 233 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.261 3.120
  ... (remaining 67904 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.600
  Find NCS groups from input model:        0.050
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
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   0.058   9043  Z= 0.203
  Angle     :  0.797   9.579  12264  Z= 0.450
  Chirality :  0.049   0.222   1338
  Planarity :  0.007   0.081   1556
  Dihedral  :  9.286  75.003   3254
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.21), residues: 1072
  helix: -1.26 (0.19), residues: 396
  sheet: -2.87 (0.33), residues: 169
  loop : -2.79 (0.23), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  20 
 TYR   0.030   0.002   TYR R 178 
 PHE   0.023   0.002   PHE R 413 
 TRP   0.024   0.002   TRP R 274 
 HIS   0.006   0.001   HIS R 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9037)
  covalent geometry    : angle       0.79683 (12252)
  SS BOND              : bond        0.00355 (    6)
  SS BOND              : angle       0.99740 (   12)
  hydrogen bonds       : bond        0.13994 (  401)
  hydrogen bonds       : angle       7.06620 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  488 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 488
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8144 (tp40) cc_final: 0.7791 (tp40)
REVERT: A  270 LEU cc_start: 0.9027 (mt) cc_final: 0.8800 (mt)
REVERT: A  272 LEU cc_start: 0.9148 (tp) cc_final: 0.8766 (tp)
REVERT: A  274 ASP cc_start: 0.7938 (t70) cc_final: 0.7648 (t0)
REVERT: A  278 ASN cc_start: 0.7815 (m-40) cc_final: 0.7275 (p0)
REVERT: A  279 ASN cc_start: 0.7763 (t0) cc_final: 0.7490 (t0)
REVERT: A  386 MET cc_start: 0.8142 (tmt) cc_final: 0.7380 (tmm)
REVERT: A  390 GLN cc_start: 0.8595 (mt0) cc_final: 0.7700 (mm-40)
REVERT: B   16 ASN cc_start: 0.8537 (m-40) cc_final: 0.8286 (m-40)
REVERT: B   75 GLN cc_start: 0.8596 (mp-120) cc_final: 0.8376 (mp10)
REVERT: B   76 ASP cc_start: 0.7059 (p0) cc_final: 0.6670 (t0)
REVERT: B  101 MET cc_start: 0.7699 (mtp) cc_final: 0.7398 (mtm)
REVERT: B  253 PHE cc_start: 0.8089 (m-80) cc_final: 0.7780 (m-80)
REVERT: B  276 VAL cc_start: 0.9110 (m) cc_final: 0.8639 (m)
REVERT: B  308 LEU cc_start: 0.8689 (mt) cc_final: 0.8349 (mp)
REVERT: N  122 THR cc_start: 0.5617 (p) cc_final: 0.4986 (p)
REVERT: R   34 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8117 (tp30)
REVERT: R   37 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8449 (tm-30)
REVERT: R   38 LYS cc_start: 0.9182 (mttt) cc_final: 0.8912 (mttt)
REVERT: R   67 ASP cc_start: 0.7810 (p0) cc_final: 0.7153 (p0)
REVERT: R   69 TYR cc_start: 0.7985 (t80) cc_final: 0.7561 (t80)
REVERT: R  163 SER cc_start: 0.9229 (m) cc_final: 0.8881 (p)
REVERT: R  179 ILE cc_start: 0.9293 (mm) cc_final: 0.8926 (mm)
REVERT: R  230 PHE cc_start: 0.7746 (t80) cc_final: 0.7087 (t80)
REVERT: R  303 MET cc_start: 0.6550 (tpp) cc_final: 0.5962 (tpp)
REVERT: R  387 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7954 (mt-10)
REVERT: R  393 PHE cc_start: 0.7554 (m-10) cc_final: 0.6916 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 488
  average time/residue: 0.1137
  time to fit residues: 72.6829
Evaluate side-chains
  264 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
N  74 ASN
R 171 HIS
R 177 ASN
R 180 HIS
R 240 ASN
R 394 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.115916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.096489 restraints weight = 30853.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.098885 restraints weight = 20582.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.100726 restraints weight = 15228.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102104 restraints weight = 12045.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.103133 restraints weight = 10034.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9043  Z= 0.187
  Angle     :  0.680  12.177  12264  Z= 0.356
  Chirality :  0.044   0.160   1338
  Planarity :  0.005   0.048   1556
  Dihedral  :  5.338  48.600   1220
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  3.91 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.24), residues: 1072
  helix:  0.64 (0.25), residues: 409
  sheet: -2.40 (0.34), residues: 191
  loop : -2.31 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 265 
 TYR   0.019   0.002   TYR A  37 
 PHE   0.022   0.002   PHE A 222 
 TRP   0.026   0.002   TRP R 284 
 HIS   0.010   0.002   HIS R 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9037)
  covalent geometry    : angle       0.67815 (12252)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       1.70459 (   12)
  hydrogen bonds       : bond        0.04173 (  401)
  hydrogen bonds       : angle       5.35089 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 329
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7971 (pp20)
REVERT: A  270 LEU cc_start: 0.9085 (mt) cc_final: 0.8840 (mt)
REVERT: A  279 ASN cc_start: 0.7691 (t0) cc_final: 0.7438 (t0)
REVERT: A  389 ARG cc_start: 0.7608 (ppt170) cc_final: 0.7068 (ppt170)
REVERT: A  390 GLN cc_start: 0.8686 (mt0) cc_final: 0.7993 (mm-40)
REVERT: B   16 ASN cc_start: 0.8497 (m-40) cc_final: 0.8267 (m-40)
REVERT: B  127 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8313 (mmtm)
REVERT: B  146 LEU cc_start: 0.8817 (mp) cc_final: 0.7844 (mp)
REVERT: B  262 MET cc_start: 0.7894 (ttm) cc_final: 0.7378 (ttp)
REVERT: B  276 VAL cc_start: 0.9249 (m) cc_final: 0.8901 (m)
REVERT: B  308 LEU cc_start: 0.8969 (mt) cc_final: 0.7992 (mt)
REVERT: B  337 LYS cc_start: 0.8882 (mptt) cc_final: 0.8362 (mptt)
REVERT: G   20 LYS cc_start: 0.7547 (pptt) cc_final: 0.6956 (tptt)
REVERT: N   18 LEU cc_start: 0.8360 (tp) cc_final: 0.7935 (tp)
REVERT: N   20 LEU cc_start: 0.8422 (mt) cc_final: 0.8158 (mt)
REVERT: N   33 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8409 (ptmm)
REVERT: N   83 MET cc_start: 0.7647 (mtm) cc_final: 0.7278 (mtm)
REVERT: R   37 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8448 (tm-30)
REVERT: R   44 ARG cc_start: 0.8968 (tmt170) cc_final: 0.8764 (tpt90)
REVERT: R   67 ASP cc_start: 0.7777 (p0) cc_final: 0.7019 (p0)
REVERT: R  163 SER cc_start: 0.9317 (m) cc_final: 0.8916 (p)
REVERT: R  184 PHE cc_start: 0.8246 (m-10) cc_final: 0.7892 (m-10)
REVERT: R  246 VAL cc_start: 0.9329 (t) cc_final: 0.9092 (p)
REVERT: R  303 MET cc_start: 0.6623 (tpp) cc_final: 0.6262 (tpp)
REVERT: R  411 LEU cc_start: 0.9426 (tp) cc_final: 0.8976 (tp)
REVERT: R  414 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7617 (mmt180)
  outliers start: 3
  outliers final: 1
  residues processed: 329
  average time/residue: 0.0992
  time to fit residues: 44.6406
Evaluate side-chains
  224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 222
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 63 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 236 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 HIS
R 171 HIS
R 173 HIS
R 240 ASN
R 304 ASN
R 407 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.113607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.094454 restraints weight = 31221.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.096739 restraints weight = 21267.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.098487 restraints weight = 15973.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.099772 restraints weight = 12718.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.100542 restraints weight = 10684.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9043  Z= 0.163
  Angle     :  0.640  10.985  12264  Z= 0.335
  Chirality :  0.043   0.138   1338
  Planarity :  0.004   0.033   1556
  Dihedral  :  5.237  39.312   1220
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.70 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.25), residues: 1072
  helix:  1.03 (0.26), residues: 397
  sheet: -2.21 (0.36), residues: 181
  loop : -2.05 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 190 
 TYR   0.016   0.002   TYR A  37 
 PHE   0.016   0.002   PHE B 253 
 TRP   0.025   0.002   TRP R 284 
 HIS   0.009   0.002   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9037)
  covalent geometry    : angle       0.63886 (12252)
  SS BOND              : bond        0.01459 (    6)
  SS BOND              : angle       1.18167 (   12)
  hydrogen bonds       : bond        0.03971 (  401)
  hydrogen bonds       : angle       5.09259 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 306
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9024 (tppp) cc_final: 0.8822 (mmmt)
REVERT: A   27 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (pp20)
REVERT: A   28 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8482 (pttm)
REVERT: A   31 GLN cc_start: 0.8622 (mm110) cc_final: 0.8135 (pt0)
REVERT: A  219 PHE cc_start: 0.6769 (m-80) cc_final: 0.6479 (m-80)
REVERT: A  266 LEU cc_start: 0.8912 (tp) cc_final: 0.8693 (tp)
REVERT: A  279 ASN cc_start: 0.7689 (t0) cc_final: 0.7457 (t0)
REVERT: A  346 LEU cc_start: 0.8922 (mt) cc_final: 0.8628 (mt)
REVERT: A  386 MET cc_start: 0.8112 (tmm) cc_final: 0.7388 (tmm)
REVERT: A  389 ARG cc_start: 0.7645 (ppt170) cc_final: 0.6900 (ppt170)
REVERT: A  390 GLN cc_start: 0.8925 (mt0) cc_final: 0.8020 (mm-40)
REVERT: B   16 ASN cc_start: 0.8530 (m-40) cc_final: 0.8304 (m-40)
REVERT: B   76 ASP cc_start: 0.7629 (p0) cc_final: 0.7151 (p0)
REVERT: B  308 LEU cc_start: 0.9031 (mt) cc_final: 0.8019 (mt)
REVERT: B  337 LYS cc_start: 0.8925 (mptt) cc_final: 0.8505 (mptt)
REVERT: B  339 TRP cc_start: 0.7337 (m100) cc_final: 0.6712 (m-10)
REVERT: G   20 LYS cc_start: 0.7475 (pptt) cc_final: 0.6945 (tptt)
REVERT: N   18 LEU cc_start: 0.8399 (tp) cc_final: 0.8037 (tp)
REVERT: N   32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8227 (m-80)
REVERT: N   33 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8310 (ptmm)
REVERT: N   34 MET cc_start: 0.8777 (mpp) cc_final: 0.8142 (mpp)
REVERT: N   83 MET cc_start: 0.7750 (mtm) cc_final: 0.7435 (mtm)
REVERT: R   37 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8580 (tm-30)
REVERT: R   67 ASP cc_start: 0.7831 (p0) cc_final: 0.7576 (p0)
REVERT: R  163 SER cc_start: 0.9313 (m) cc_final: 0.8965 (p)
REVERT: R  184 PHE cc_start: 0.8238 (m-10) cc_final: 0.7941 (m-10)
REVERT: R  297 TRP cc_start: 0.4928 (t60) cc_final: 0.4544 (t60)
REVERT: R  415 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8827 (ptpp)
  outliers start: 1
  outliers final: 0
  residues processed: 306
  average time/residue: 0.0926
  time to fit residues: 39.5317
Evaluate side-chains
  226 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 33 optimal weight:    0.3980
   chunk 88 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 41 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
R 171 HIS
R 173 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.110226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.091519 restraints weight = 32217.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.093732 restraints weight = 21567.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.095387 restraints weight = 15983.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.096453 restraints weight = 12734.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.097340 restraints weight = 10807.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.6122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9043  Z= 0.169
  Angle     :  0.638  10.690  12264  Z= 0.336
  Chirality :  0.043   0.134   1338
  Planarity :  0.004   0.031   1556
  Dihedral  :  5.376  42.140   1220
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.25), residues: 1072
  helix:  0.99 (0.26), residues: 403
  sheet: -1.94 (0.37), residues: 173
  loop : -1.83 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R  48 
 TYR   0.016   0.002   TYR R 220 
 PHE   0.012   0.002   PHE B 151 
 TRP   0.019   0.002   TRP R 284 
 HIS   0.010   0.002   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9037)
  covalent geometry    : angle       0.63709 (12252)
  SS BOND              : bond        0.00171 (    6)
  SS BOND              : angle       1.20318 (   12)
  hydrogen bonds       : bond        0.03969 (  401)
  hydrogen bonds       : angle       4.98183 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8137 (pm20) cc_final: 0.7455 (pp20)
REVERT: A   31 GLN cc_start: 0.8639 (mm110) cc_final: 0.8315 (pt0)
REVERT: A  223 ASP cc_start: 0.7395 (t0) cc_final: 0.7179 (t70)
REVERT: A  272 LEU cc_start: 0.9357 (tp) cc_final: 0.9055 (tp)
REVERT: A  346 LEU cc_start: 0.8914 (mt) cc_final: 0.8620 (mt)
REVERT: A  390 GLN cc_start: 0.9001 (mt0) cc_final: 0.8708 (mt0)
REVERT: B   16 ASN cc_start: 0.8617 (m-40) cc_final: 0.8373 (m-40)
REVERT: B   50 THR cc_start: 0.8407 (m) cc_final: 0.7889 (p)
REVERT: B   76 ASP cc_start: 0.7775 (p0) cc_final: 0.7409 (p0)
REVERT: B  101 MET cc_start: 0.8510 (mpp) cc_final: 0.8183 (mtm)
REVERT: B  121 CYS cc_start: 0.8434 (m) cc_final: 0.8217 (m)
REVERT: B  175 GLN cc_start: 0.8282 (mp-120) cc_final: 0.7969 (mp10)
REVERT: B  308 LEU cc_start: 0.8952 (mt) cc_final: 0.7863 (mp)
REVERT: B  337 LYS cc_start: 0.8948 (mptt) cc_final: 0.8555 (mptt)
REVERT: B  339 TRP cc_start: 0.7435 (m100) cc_final: 0.7096 (m-10)
REVERT: G   20 LYS cc_start: 0.7639 (pptt) cc_final: 0.7098 (tptt)
REVERT: N   32 TYR cc_start: 0.8753 (m-80) cc_final: 0.8278 (m-80)
REVERT: N   34 MET cc_start: 0.8818 (mpp) cc_final: 0.8136 (mpp)
REVERT: N   77 ASN cc_start: 0.7997 (t0) cc_final: 0.7310 (t0)
REVERT: R   34 GLU cc_start: 0.8166 (tp30) cc_final: 0.7966 (tp30)
REVERT: R   37 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8583 (tm-30)
REVERT: R   38 LYS cc_start: 0.9069 (pttm) cc_final: 0.8482 (pttm)
REVERT: R   67 ASP cc_start: 0.8172 (p0) cc_final: 0.7733 (p0)
REVERT: R  163 SER cc_start: 0.9323 (m) cc_final: 0.9019 (p)
REVERT: R  184 PHE cc_start: 0.8296 (m-10) cc_final: 0.7968 (m-10)
REVERT: R  230 PHE cc_start: 0.8188 (t80) cc_final: 0.7521 (t80)
REVERT: R  297 TRP cc_start: 0.5110 (t60) cc_final: 0.4672 (t60)
REVERT: R  360 LEU cc_start: 0.9038 (mt) cc_final: 0.8784 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.0903
  time to fit residues: 37.5078
Evaluate side-chains
  212 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 268 ASN
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 171 HIS
R 210 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.109868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.090772 restraints weight = 32231.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.093047 restraints weight = 21589.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.094704 restraints weight = 16048.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.095660 restraints weight = 12786.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.096504 restraints weight = 10970.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.6371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9043  Z= 0.164
  Angle     :  0.617   7.878  12264  Z= 0.327
  Chirality :  0.043   0.139   1338
  Planarity :  0.004   0.031   1556
  Dihedral  :  5.371  44.331   1220
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.22 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.25), residues: 1072
  helix:  1.07 (0.25), residues: 402
  sheet: -1.89 (0.38), residues: 177
  loop : -1.79 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.021   0.002   TYR R 220 
 PHE   0.019   0.002   PHE R 315 
 TRP   0.014   0.002   TRP R 284 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9037)
  covalent geometry    : angle       0.61679 (12252)
  SS BOND              : bond        0.00788 (    6)
  SS BOND              : angle       1.05087 (   12)
  hydrogen bonds       : bond        0.03936 (  401)
  hydrogen bonds       : angle       4.95793 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 292
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.7675 (t0) cc_final: 0.7426 (t0)
REVERT: A  284 ASP cc_start: 0.7572 (m-30) cc_final: 0.7360 (m-30)
REVERT: A  346 LEU cc_start: 0.8885 (mt) cc_final: 0.8671 (mt)
REVERT: A  386 MET cc_start: 0.8117 (tmm) cc_final: 0.7790 (tmm)
REVERT: A  390 GLN cc_start: 0.9044 (mt0) cc_final: 0.8778 (mt0)
REVERT: B   50 THR cc_start: 0.8350 (m) cc_final: 0.8124 (p)
REVERT: B   76 ASP cc_start: 0.7550 (p0) cc_final: 0.6990 (p0)
REVERT: B  254 ASP cc_start: 0.7174 (t70) cc_final: 0.6726 (t0)
REVERT: B  308 LEU cc_start: 0.8902 (mt) cc_final: 0.7757 (mp)
REVERT: B  337 LYS cc_start: 0.8869 (mptt) cc_final: 0.8524 (mmtm)
REVERT: N   20 LEU cc_start: 0.8684 (mt) cc_final: 0.8441 (mt)
REVERT: N   32 TYR cc_start: 0.8689 (m-80) cc_final: 0.8234 (m-80)
REVERT: N   34 MET cc_start: 0.8793 (mpp) cc_final: 0.8022 (mpp)
REVERT: N   77 ASN cc_start: 0.7869 (t0) cc_final: 0.7079 (t0)
REVERT: R   37 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8538 (tm-30)
REVERT: R   69 TYR cc_start: 0.8256 (t80) cc_final: 0.8037 (t80)
REVERT: R  163 SER cc_start: 0.9324 (m) cc_final: 0.9038 (p)
REVERT: R  177 ASN cc_start: 0.9282 (m110) cc_final: 0.9035 (m110)
REVERT: R  182 ASN cc_start: 0.8878 (m-40) cc_final: 0.8279 (m-40)
REVERT: R  184 PHE cc_start: 0.8252 (m-10) cc_final: 0.7906 (m-10)
REVERT: R  230 PHE cc_start: 0.8312 (t80) cc_final: 0.7700 (t80)
REVERT: R  297 TRP cc_start: 0.5106 (t60) cc_final: 0.4730 (t60)
REVERT: R  414 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7562 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 292
  average time/residue: 0.0892
  time to fit residues: 36.8244
Evaluate side-chains
  222 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0980
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 73 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 66 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B   6 GLN
B 268 ASN
N  39 GLN
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 210 GLN
R 363 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.109271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.089991 restraints weight = 31714.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.092317 restraints weight = 20967.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.094015 restraints weight = 15390.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.095216 restraints weight = 12167.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.095949 restraints weight = 10229.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.6668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9043  Z= 0.172
  Angle     :  0.629   8.115  12264  Z= 0.333
  Chirality :  0.044   0.138   1338
  Planarity :  0.004   0.041   1556
  Dihedral  :  5.420  45.577   1220
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.25), residues: 1072
  helix:  1.09 (0.25), residues: 402
  sheet: -1.76 (0.37), residues: 187
  loop : -1.68 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B   8 
 TYR   0.022   0.002   TYR R 220 
 PHE   0.024   0.002   PHE A 222 
 TRP   0.026   0.002   TRP B 339 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9037)
  covalent geometry    : angle       0.62854 (12252)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       1.02261 (   12)
  hydrogen bonds       : bond        0.03968 (  401)
  hydrogen bonds       : angle       4.93151 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8190 (pp20) cc_final: 0.7840 (pp20)
REVERT: A   28 LYS cc_start: 0.8926 (ptpp) cc_final: 0.8530 (pttm)
REVERT: A   31 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8295 (pm20)
REVERT: A  223 ASP cc_start: 0.7537 (t0) cc_final: 0.7297 (t0)
REVERT: A  270 LEU cc_start: 0.9107 (mt) cc_final: 0.8898 (mt)
REVERT: A  346 LEU cc_start: 0.8906 (mt) cc_final: 0.8695 (mt)
REVERT: A  386 MET cc_start: 0.8119 (tmm) cc_final: 0.7549 (tmm)
REVERT: A  387 HIS cc_start: 0.8551 (m-70) cc_final: 0.8271 (m-70)
REVERT: A  390 GLN cc_start: 0.9050 (mt0) cc_final: 0.8426 (mt0)
REVERT: B   76 ASP cc_start: 0.7590 (p0) cc_final: 0.7048 (p0)
REVERT: B  186 ASP cc_start: 0.7067 (m-30) cc_final: 0.6785 (m-30)
REVERT: B  254 ASP cc_start: 0.7054 (t70) cc_final: 0.6632 (t0)
REVERT: B  261 LEU cc_start: 0.9165 (mm) cc_final: 0.8963 (mm)
REVERT: B  311 HIS cc_start: 0.6565 (m-70) cc_final: 0.6216 (m-70)
REVERT: B  337 LYS cc_start: 0.9074 (mptt) cc_final: 0.8564 (mptt)
REVERT: G   20 LYS cc_start: 0.7525 (pptt) cc_final: 0.6962 (tptt)
REVERT: N   20 LEU cc_start: 0.8691 (mt) cc_final: 0.8347 (mt)
REVERT: N   32 TYR cc_start: 0.8651 (m-80) cc_final: 0.8245 (m-80)
REVERT: N   34 MET cc_start: 0.8764 (mpp) cc_final: 0.7927 (mpp)
REVERT: N   77 ASN cc_start: 0.7911 (t0) cc_final: 0.7077 (t0)
REVERT: N  120 GLN cc_start: 0.7020 (pp30) cc_final: 0.6558 (pp30)
REVERT: R   37 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8479 (tm-30)
REVERT: R   38 LYS cc_start: 0.9058 (pttt) cc_final: 0.8761 (pttt)
REVERT: R   67 ASP cc_start: 0.8064 (p0) cc_final: 0.7550 (p0)
REVERT: R  163 SER cc_start: 0.9277 (m) cc_final: 0.8973 (p)
REVERT: R  176 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.7841 (ptt-90)
REVERT: R  177 ASN cc_start: 0.9274 (m110) cc_final: 0.8851 (m110)
REVERT: R  182 ASN cc_start: 0.8852 (m-40) cc_final: 0.8273 (m-40)
REVERT: R  184 PHE cc_start: 0.8253 (m-10) cc_final: 0.7882 (m-10)
REVERT: R  230 PHE cc_start: 0.8360 (t80) cc_final: 0.7901 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 295
  average time/residue: 0.0861
  time to fit residues: 36.2534
Evaluate side-chains
  211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 142 HIS
B 268 ASN
N  39 GLN
R 171 HIS
R 173 HIS
R 210 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.111499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.092862 restraints weight = 31489.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.095094 restraints weight = 21100.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.096510 restraints weight = 15632.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097813 restraints weight = 12614.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.098558 restraints weight = 10576.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.6756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9043  Z= 0.127
  Angle     :  0.631   8.595  12264  Z= 0.331
  Chirality :  0.044   0.150   1338
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.260  39.269   1220
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.25), residues: 1072
  helix:  1.21 (0.25), residues: 403
  sheet: -1.74 (0.37), residues: 179
  loop : -1.69 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R  48 
 TYR   0.020   0.002   TYR R 220 
 PHE   0.026   0.001   PHE A 238 
 TRP   0.035   0.002   TRP R 297 
 HIS   0.008   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9037)
  covalent geometry    : angle       0.63033 (12252)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       1.21094 (   12)
  hydrogen bonds       : bond        0.03865 (  401)
  hydrogen bonds       : angle       4.86279 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.7386 (t0) cc_final: 0.7160 (t0)
REVERT: A  272 LEU cc_start: 0.9377 (tp) cc_final: 0.9158 (tp)
REVERT: A  279 ASN cc_start: 0.7809 (t0) cc_final: 0.7549 (t0)
REVERT: A  346 LEU cc_start: 0.8894 (mt) cc_final: 0.8594 (mt)
REVERT: A  386 MET cc_start: 0.8067 (tmm) cc_final: 0.7570 (tmm)
REVERT: A  387 HIS cc_start: 0.8565 (m-70) cc_final: 0.8096 (m-70)
REVERT: A  390 GLN cc_start: 0.8965 (mt0) cc_final: 0.8264 (mt0)
REVERT: B   52 ARG cc_start: 0.7439 (mpp80) cc_final: 0.7193 (mpp80)
REVERT: B   76 ASP cc_start: 0.7264 (p0) cc_final: 0.6533 (p0)
REVERT: B  160 SER cc_start: 0.8395 (p) cc_final: 0.7967 (p)
REVERT: B  254 ASP cc_start: 0.7089 (t70) cc_final: 0.6615 (t0)
REVERT: B  337 LYS cc_start: 0.8997 (mptt) cc_final: 0.8477 (mmtm)
REVERT: G   20 LYS cc_start: 0.7578 (pptt) cc_final: 0.7110 (tptt)
REVERT: N   20 LEU cc_start: 0.8720 (mt) cc_final: 0.8362 (mt)
REVERT: N   32 TYR cc_start: 0.8627 (m-80) cc_final: 0.8358 (m-80)
REVERT: N   34 MET cc_start: 0.8739 (mpp) cc_final: 0.7850 (mpp)
REVERT: N   77 ASN cc_start: 0.7907 (t0) cc_final: 0.7230 (t0)
REVERT: R   37 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8592 (tm-30)
REVERT: R   38 LYS cc_start: 0.9069 (pttt) cc_final: 0.8809 (pttt)
REVERT: R   48 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8312 (tpt90)
REVERT: R   67 ASP cc_start: 0.8191 (p0) cc_final: 0.7720 (p0)
REVERT: R  176 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7810 (ptt-90)
REVERT: R  177 ASN cc_start: 0.9282 (m110) cc_final: 0.8904 (m110)
REVERT: R  230 PHE cc_start: 0.8325 (t80) cc_final: 0.7883 (t80)
REVERT: R  284 TRP cc_start: 0.7469 (t60) cc_final: 0.6755 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.0903
  time to fit residues: 36.3300
Evaluate side-chains
  212 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
A 220 HIS
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  54 HIS
B 230 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN
R 173 HIS
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.109925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.090853 restraints weight = 31445.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.093174 restraints weight = 20744.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.094737 restraints weight = 15248.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.095974 restraints weight = 12173.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.096937 restraints weight = 10240.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.7022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9043  Z= 0.163
  Angle     :  0.655   8.821  12264  Z= 0.347
  Chirality :  0.045   0.233   1338
  Planarity :  0.004   0.086   1556
  Dihedral  :  5.479  47.223   1220
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.25), residues: 1072
  helix:  1.09 (0.25), residues: 404
  sheet: -1.56 (0.37), residues: 186
  loop : -1.61 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R  48 
 TYR   0.022   0.002   TYR R 220 
 PHE   0.028   0.002   PHE A 222 
 TRP   0.028   0.002   TRP B 339 
 HIS   0.009   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9037)
  covalent geometry    : angle       0.65390 (12252)
  SS BOND              : bond        0.00400 (    6)
  SS BOND              : angle       1.43997 (   12)
  hydrogen bonds       : bond        0.04005 (  401)
  hydrogen bonds       : angle       4.93199 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8954 (ptpp) cc_final: 0.8701 (pttm)
REVERT: A  223 ASP cc_start: 0.7541 (t0) cc_final: 0.7316 (t0)
REVERT: A  278 ASN cc_start: 0.8156 (m-40) cc_final: 0.7505 (m-40)
REVERT: A  346 LEU cc_start: 0.8911 (mt) cc_final: 0.8630 (mt)
REVERT: A  358 TYR cc_start: 0.6466 (m-10) cc_final: 0.6025 (m-10)
REVERT: A  386 MET cc_start: 0.8087 (tmm) cc_final: 0.7567 (tmm)
REVERT: A  387 HIS cc_start: 0.8558 (m-70) cc_final: 0.8073 (m-70)
REVERT: A  390 GLN cc_start: 0.8956 (mt0) cc_final: 0.8275 (mt0)
REVERT: B   16 ASN cc_start: 0.8672 (m-40) cc_final: 0.8448 (m-40)
REVERT: B   76 ASP cc_start: 0.7301 (p0) cc_final: 0.6535 (p0)
REVERT: B  186 ASP cc_start: 0.7067 (m-30) cc_final: 0.6832 (m-30)
REVERT: B  254 ASP cc_start: 0.7192 (t70) cc_final: 0.6794 (t0)
REVERT: B  337 LYS cc_start: 0.8991 (mptt) cc_final: 0.8669 (mmtm)
REVERT: N   32 TYR cc_start: 0.8657 (m-80) cc_final: 0.8293 (m-80)
REVERT: N   34 MET cc_start: 0.8770 (mpp) cc_final: 0.7874 (mpp)
REVERT: N   77 ASN cc_start: 0.7967 (t0) cc_final: 0.7249 (t0)
REVERT: R   37 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8525 (tm-30)
REVERT: R   38 LYS cc_start: 0.9089 (pttt) cc_final: 0.8704 (pttt)
REVERT: R  174 CYS cc_start: 0.8585 (t) cc_final: 0.8381 (t)
REVERT: R  176 ARG cc_start: 0.8250 (ptt-90) cc_final: 0.7766 (ptt-90)
REVERT: R  177 ASN cc_start: 0.9273 (m110) cc_final: 0.8819 (m110)
REVERT: R  179 ILE cc_start: 0.9383 (mm) cc_final: 0.8813 (mm)
REVERT: R  182 ASN cc_start: 0.8814 (m-40) cc_final: 0.8295 (m-40)
REVERT: R  230 PHE cc_start: 0.8322 (t80) cc_final: 0.7866 (t80)
REVERT: R  231 LEU cc_start: 0.9195 (tt) cc_final: 0.8767 (tt)
REVERT: R  284 TRP cc_start: 0.7626 (t60) cc_final: 0.6649 (t60)
REVERT: R  412 GLU cc_start: 0.8096 (mp0) cc_final: 0.7617 (mp0)
REVERT: R  414 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7921 (mmt-90)
REVERT: R  415 LYS cc_start: 0.9164 (ptpp) cc_final: 0.8677 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.0892
  time to fit residues: 35.1337
Evaluate side-chains
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    0.1980
   chunk 79 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0370
   chunk 95 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    1.8464

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 110 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  74 ASN
R 173 HIS
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 374 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.110895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.091969 restraints weight = 31152.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.094303 restraints weight = 20465.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.095914 restraints weight = 14941.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.097185 restraints weight = 11864.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.097911 restraints weight = 9930.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.7152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9043  Z= 0.144
  Angle     :  0.641   9.050  12264  Z= 0.337
  Chirality :  0.045   0.164   1338
  Planarity :  0.004   0.057   1556
  Dihedral  :  5.418  43.133   1220
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.25), residues: 1072
  helix:  1.16 (0.25), residues: 403
  sheet: -1.49 (0.37), residues: 180
  loop : -1.57 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 389 
 TYR   0.022   0.002   TYR R 220 
 PHE   0.030   0.002   PHE A 222 
 TRP   0.027   0.002   TRP R 284 
 HIS   0.008   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9037)
  covalent geometry    : angle       0.64054 (12252)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       1.28585 (   12)
  hydrogen bonds       : bond        0.03933 (  401)
  hydrogen bonds       : angle       4.82122 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.9286 (tp) cc_final: 0.9001 (tp)
REVERT: A  346 LEU cc_start: 0.8924 (mt) cc_final: 0.8641 (mt)
REVERT: A  386 MET cc_start: 0.8010 (tmm) cc_final: 0.7475 (tmm)
REVERT: A  387 HIS cc_start: 0.8506 (m-70) cc_final: 0.8122 (m-70)
REVERT: A  389 ARG cc_start: 0.7862 (ppt170) cc_final: 0.7646 (ppt170)
REVERT: A  390 GLN cc_start: 0.8923 (mt0) cc_final: 0.8321 (mt0)
REVERT: B   16 ASN cc_start: 0.8590 (m-40) cc_final: 0.8389 (m-40)
REVERT: B   76 ASP cc_start: 0.7397 (p0) cc_final: 0.6584 (t0)
REVERT: B  186 ASP cc_start: 0.7143 (m-30) cc_final: 0.6942 (m-30)
REVERT: B  254 ASP cc_start: 0.7263 (t70) cc_final: 0.6836 (t0)
REVERT: G   32 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8202 (ptpp)
REVERT: N   32 TYR cc_start: 0.8631 (m-80) cc_final: 0.8283 (m-80)
REVERT: N   34 MET cc_start: 0.8796 (mpp) cc_final: 0.7762 (mpp)
REVERT: N   73 ASP cc_start: 0.7808 (m-30) cc_final: 0.6792 (m-30)
REVERT: N   77 ASN cc_start: 0.8023 (t0) cc_final: 0.7254 (t0)
REVERT: R   37 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8604 (tm-30)
REVERT: R   38 LYS cc_start: 0.9095 (pttt) cc_final: 0.8751 (pttt)
REVERT: R  174 CYS cc_start: 0.8536 (t) cc_final: 0.8317 (t)
REVERT: R  176 ARG cc_start: 0.8217 (ptt-90) cc_final: 0.7751 (ptt-90)
REVERT: R  177 ASN cc_start: 0.9292 (m110) cc_final: 0.8832 (m110)
REVERT: R  230 PHE cc_start: 0.8310 (t80) cc_final: 0.7845 (t80)
REVERT: R  231 LEU cc_start: 0.9156 (tt) cc_final: 0.8765 (tt)
REVERT: R  284 TRP cc_start: 0.7646 (t60) cc_final: 0.6687 (t60)
REVERT: R  412 GLU cc_start: 0.8052 (mp0) cc_final: 0.7482 (mp0)
REVERT: R  414 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7909 (mmt-90)
REVERT: R  415 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8710 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.0863
  time to fit residues: 34.3285
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0980
   chunk 82 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  35 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 374 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.109394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.090538 restraints weight = 31147.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.092818 restraints weight = 20687.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.094419 restraints weight = 15301.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.095374 restraints weight = 12205.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.096329 restraints weight = 10472.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9043  Z= 0.164
  Angle     :  0.673   8.866  12264  Z= 0.354
  Chirality :  0.046   0.183   1338
  Planarity :  0.004   0.048   1556
  Dihedral  :  5.505  47.331   1220
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.25), residues: 1072
  helix:  1.04 (0.25), residues: 403
  sheet: -1.45 (0.37), residues: 183
  loop : -1.52 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R  48 
 TYR   0.022   0.002   TYR R 220 
 PHE   0.033   0.002   PHE A 222 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.011   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9037)
  covalent geometry    : angle       0.67260 (12252)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       1.05786 (   12)
  hydrogen bonds       : bond        0.04027 (  401)
  hydrogen bonds       : angle       4.93826 ( 1170)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.7510 (t0) cc_final: 0.7245 (t0)
REVERT: A  346 LEU cc_start: 0.8942 (mt) cc_final: 0.8639 (mt)
REVERT: A  349 SER cc_start: 0.9054 (t) cc_final: 0.8666 (p)
REVERT: A  386 MET cc_start: 0.8043 (tmm) cc_final: 0.7767 (tmm)
REVERT: A  387 HIS cc_start: 0.8531 (m-70) cc_final: 0.7996 (m-70)
REVERT: A  390 GLN cc_start: 0.8940 (mt0) cc_final: 0.8317 (mt0)
REVERT: B   76 ASP cc_start: 0.7527 (p0) cc_final: 0.6704 (t0)
REVERT: B  254 ASP cc_start: 0.7173 (t70) cc_final: 0.6827 (t0)
REVERT: B  337 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8551 (mmtm)
REVERT: N   32 TYR cc_start: 0.8573 (m-80) cc_final: 0.8267 (m-80)
REVERT: N   34 MET cc_start: 0.8814 (mpp) cc_final: 0.7743 (mpp)
REVERT: N   77 ASN cc_start: 0.7901 (t0) cc_final: 0.7483 (t0)
REVERT: R   37 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8526 (tm-30)
REVERT: R   38 LYS cc_start: 0.9114 (pttt) cc_final: 0.8684 (pttt)
REVERT: R  174 CYS cc_start: 0.8598 (t) cc_final: 0.8324 (t)
REVERT: R  176 ARG cc_start: 0.8195 (ptt-90) cc_final: 0.7753 (ptt-90)
REVERT: R  177 ASN cc_start: 0.9272 (m110) cc_final: 0.8785 (m110)
REVERT: R  230 PHE cc_start: 0.8297 (t80) cc_final: 0.8085 (t80)
REVERT: R  284 TRP cc_start: 0.7742 (t60) cc_final: 0.7374 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.0799
  time to fit residues: 31.6983
Evaluate side-chains
  209 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 85 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0370
   chunk 49 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    2.4066

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  74 ASN
R 173 HIS
** R 210 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 = 0.3977 r_free = 0.3977 target = 0.109278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.090815 restraints weight = 31507.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.093043 restraints weight = 21074.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.094627 restraints weight = 15620.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.095822 restraints weight = 12497.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.096525 restraints weight = 10504.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.7408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9043  Z= 0.165
  Angle     :  0.665   8.496  12264  Z= 0.351
  Chirality :  0.046   0.156   1338
  Planarity :  0.004   0.041   1556
  Dihedral  :  5.490  46.328   1220
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.25), residues: 1072
  helix:  1.11 (0.25), residues: 402
  sheet: -1.38 (0.37), residues: 186
  loop : -1.49 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  44 
 TYR   0.022   0.002   TYR R 220 
 PHE   0.036   0.002   PHE A 222 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9037)
  covalent geometry    : angle       0.66482 (12252)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.99307 (   12)
  hydrogen bonds       : bond        0.04064 (  401)
  hydrogen bonds       : angle       4.91523 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1705.31 seconds
wall clock time: 30 minutes 16.24 seconds (1816.24 seconds total)