Starting phenix.real_space_refine
on Fri Aug 22 23:42:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkz_36384/08_2025/8jkz_36384.map"
  }
  resolution = 3.6
  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=   0.002 sd=   0.027
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
     P       2      5.49       5
     S      33      5.16       5
     C    5404      2.51       5
     N    1443      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8444
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4674
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 23, 'TRANS': 560}
    Chain: "B"
      Number of atoms: 3726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3726
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 28, 'TRANS': 440}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.23
  Number of scatterers: 8444
  At special positions: 0
  Unit cell: (78.12, 98.28, 122.64, 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      33     16.00
     P       2     15.00
     O    1562      8.00
     N    1443      7.00
     C    5404      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.48
  Conformation dependent library (CDL) restraints added in 403.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 11 sheets defined
      41.5% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 16
      removed outlier: 3.550A  pdb=" N   GLN A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   HIS A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   TYR A  13 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 33
      removed outlier: 3.621A  pdb=" N   THR A  28 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A  29 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG A  30 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   SER A  31 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY A  33 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 49
    Processing helix  chain 'A' and resid 65 through 78
      removed outlier: 3.600A  pdb=" N   SER A  69 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 98
    Processing helix  chain 'A' and resid 100 through 112
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 168 through 176
      removed outlier: 3.826A  pdb=" N   SER A 172 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 195
    Processing helix  chain 'A' and resid 198 through 217
    Processing helix  chain 'A' and resid 231 through 243
    Processing helix  chain 'A' and resid 257 through 261
    Processing helix  chain 'A' and resid 262 through 276
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 4.075A  pdb=" N   GLN A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 310
      removed outlier: 3.547A  pdb=" N   ARG A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 366
    Processing helix  chain 'A' and resid 383 through 390
    Processing helix  chain 'A' and resid 406 through 414
      removed outlier: 3.965A  pdb=" N   SER A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 431
    Processing helix  chain 'A' and resid 439 through 443
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 532 through 548
      removed outlier: 3.574A  pdb=" N   GLN A 538 " --> pdb=" O   GLN A 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 3.837A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 106
      removed outlier: 3.699A  pdb=" N   ARG B 106 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.948A  pdb=" N   VAL B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 138
      removed outlier: 3.602A  pdb=" N   ALA B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 156
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 184 through 189
      removed outlier: 4.118A  pdb=" N   LEU B 188 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 209
      removed outlier: 3.547A  pdb=" N   VAL B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 202 " --> pdb=" O   TRP B 198 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 276 through 295
    Processing helix  chain 'B' and resid 312 through 321
      removed outlier: 3.514A  pdb=" N   GLN B 317 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 430
      removed outlier: 4.150A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 458
      removed outlier: 3.624A  pdb=" N   VAL B 447 " --> pdb=" O   PRO B 443 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLN B 458 " --> pdb=" O   ASP B 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184
      removed outlier: 6.404A  pdb=" N   VAL A 138 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   MET A  20 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   PHE A 139 " --> pdb=" O   MET A  20 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   TRP A  22 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 252
      removed outlier: 6.546A  pdb=" N   LEU A 251 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580
      removed outlier: 3.610A  pdb=" N   ALA A 330 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL B 345 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338
      removed outlier: 4.550A  pdb=" N   LEU A 501 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380
      removed outlier: 3.611A  pdb=" N   CYS A 345 " --> pdb=" O   TYR A 402 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561
      removed outlier: 3.548A  pdb=" N   ALA A 569 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.331A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.331A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27
      removed outlier: 3.748A  pdb=" N   ARG B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.669A  pdb=" N   VAL B  50 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ARG B  51 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA B  53 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   TYR B 149 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU B  55 " --> pdb=" O   TYR B 149 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU B 146 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ILE B 183 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   VAL B 148 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 267

    346 hydrogen bonds defined for protein.
    990 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: 1.30

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1378
        1.31 -     1.43: 2382
        1.43 -     1.56: 4838
        1.56 -     1.68: 8
        1.68 -     1.81: 51
  Bond restraints: 8657
  Sorted by residual:
  bond pdb=" C2D NAD A 601 "
       pdb=" C3D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.531  1.243  0.288 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" C4B NAD A 601 "
       pdb=" O4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.433  1.681 -0.248 2.00e-02 2.50e+03 1.54e+02
  bond pdb=" C3B NAD A 601 "
       pdb=" C4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.523  1.281  0.242 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" C4D NAD A 601 "
       pdb=" O4D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.445  1.274  0.171 2.00e-02 2.50e+03 7.31e+01
  bond pdb=" C7N NAD A 601 "
       pdb=" N7N NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.328  1.473 -0.145 2.00e-02 2.50e+03 5.25e+01
  ... (remaining 8652 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 11571
        2.64 -     5.28: 154
        5.28 -     7.93: 15
        7.93 -    10.57: 5
       10.57 -    13.21: 3
  Bond angle restraints: 11748
  Sorted by residual:
  angle pdb=" C   ILE A 390 "
        pdb=" N   PHE A 391 "
        pdb=" CA  PHE A 391 "
      ideal   model   delta    sigma   weight residual
     121.54  131.43   -9.89 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" O1A NAD A 601 "
        pdb=" PA  NAD A 601 "
        pdb=" O2A NAD A 601 "
      ideal   model   delta    sigma   weight residual
     122.64  109.43   13.21 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" C   ALA B   9 "
        pdb=" CA  ALA B   9 "
        pdb=" CB  ALA B   9 "
      ideal   model   delta    sigma   weight residual
     116.34  110.45    5.89 1.40e+00 5.10e-01 1.77e+01
  angle pdb=" O3  NAD A 601 "
        pdb=" PN  NAD A 601 "
        pdb=" O5D NAD A 601 "
      ideal   model   delta    sigma   weight residual
      98.00  109.75  -11.75 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" O1N NAD A 601 "
        pdb=" PN  NAD A 601 "
        pdb=" O2N NAD A 601 "
      ideal   model   delta    sigma   weight residual
     120.02  109.43   10.59 3.00e+00 1.11e-01 1.25e+01
  ... (remaining 11743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4401
       17.98 -    35.96: 593
       35.96 -    53.95: 154
       53.95 -    71.93: 32
       71.93 -    89.91: 15
  Dihedral angle restraints: 5195
    sinusoidal: 2120
      harmonic: 3075
  Sorted by residual:
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   PRO B  47 "
           pdb=" CA  PRO B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.47   27.53     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  TYR A 374 "
           pdb=" C   TYR A 374 "
           pdb=" N   THR A 375 "
           pdb=" CA  THR A 375 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.19   18.81     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  MET A 132 "
           pdb=" C   MET A 132 "
           pdb=" N   ASN A 133 "
           pdb=" CA  ASN A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.98  -18.02     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 5192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1141
       0.070 -    0.140: 130
       0.140 -    0.210: 8
       0.210 -    0.280: 1
       0.280 -    0.351: 1
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" C3D NAD A 601 "
            pdb=" C2D NAD A 601 "
            pdb=" C4D NAD A 601 "
            pdb=" O3D NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.38   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" C3B NAD A 601 "
            pdb=" C2B NAD A 601 "
            pdb=" C4B NAD A 601 "
            pdb=" O3B NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.44   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C2D NAD A 601 "
            pdb=" C1D NAD A 601 "
            pdb=" C3D NAD A 601 "
            pdb=" O2D NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.37   -0.19 2.00e-01 2.50e+01 9.50e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 206 "    0.187 9.50e-02 1.11e+02   8.39e-02 4.33e+00
        pdb=" NE  ARG A 206 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 206 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 391 "   -0.011 2.00e-02 2.50e+03   1.52e-02 4.06e+00
        pdb=" CG  PHE A 391 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 391 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 391 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 391 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 391 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 391 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 390 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ILE A 390 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE A 390 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 391 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1203
        2.76 -     3.29: 8017
        3.29 -     3.83: 13547
        3.83 -     4.36: 15536
        4.36 -     4.90: 27371
  Nonbonded interactions: 65674
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  83 "
            pdb=" O   ASN B 436 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR B 277 "
            pdb=" OD2 ASP B 321 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   ALA A 578 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU B 330 "
            pdb=" NH1 ARG B 411 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" ND2 ASN B 389 "
            pdb=" OE1 GLN B 392 "
     model   vdw
     2.267 3.120
  ... (remaining 65669 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.040
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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      :  0.007   0.288   8657  Z= 0.383
  Angle     :  0.735  13.209  11748  Z= 0.398
  Chirality :  0.045   0.351   1281
  Planarity :  0.004   0.084   1505
  Dihedral  : 17.975  89.910   3219
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.01 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 26.00 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.21 (0.27), residues: 1049
  helix:  0.80 (0.27), residues: 388
  sheet: -0.76 (0.40), residues: 189
  loop : -2.25 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  69 
 TYR   0.013   0.001   TYR B 149 
 PHE   0.035   0.002   PHE A 391 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.007   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 ( 8657)
  covalent geometry    : angle       0.73534 (11748)
  hydrogen bonds       : bond        0.18328 (  323)
  hydrogen bonds       : angle       6.48013 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 92
  average time/residue: 0.1215
  time to fit residues: 14.8281
Evaluate side-chains
  78 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain B residue  257 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0470
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.1284

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 317 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.154405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116072 restraints weight = 12027.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.113652 restraints weight = 12741.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115292 restraints weight = 14030.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.115662 restraints weight = 9660.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.116288 restraints weight = 9400.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8657  Z= 0.142
  Angle     :  0.578   8.553  11748  Z= 0.305
  Chirality :  0.042   0.160   1281
  Planarity :  0.004   0.039   1505
  Dihedral  :  7.101  63.997   1212
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.72 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.78 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.27), residues: 1049
  helix:  1.12 (0.28), residues: 389
  sheet: -0.74 (0.39), residues: 186
  loop : -2.23 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 438 
 TYR   0.015   0.001   TYR B 366 
 PHE   0.013   0.001   PHE A 328 
 TRP   0.010   0.001   TRP B 377 
 HIS   0.007   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8657)
  covalent geometry    : angle       0.57791 (11748)
  hydrogen bonds       : bond        0.04333 (  323)
  hydrogen bonds       : angle       4.58007 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 81
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7266 (t80)
REVERT: A  112 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4258 (tt)
  outliers start: 33
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0941
  time to fit residues: 14.3551
Evaluate side-chains
  90 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0040
   overall best weight:    1.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B  45 ASN
B 339 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.152340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.113923 restraints weight = 11860.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.111047 restraints weight = 14273.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.112969 restraints weight = 14079.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.113798 restraints weight = 9301.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.114416 restraints weight = 8858.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8657  Z= 0.168
  Angle     :  0.585   8.254  11748  Z= 0.309
  Chirality :  0.043   0.157   1281
  Planarity :  0.004   0.038   1505
  Dihedral  :  6.657  59.104   1209
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.49 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 22.46 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.27), residues: 1049
  helix:  1.21 (0.28), residues: 389
  sheet: -0.85 (0.39), residues: 187
  loop : -2.23 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  69 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.013   0.002   PHE B 452 
 TRP   0.014   0.001   TRP B 377 
 HIS   0.007   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8657)
  covalent geometry    : angle       0.58545 (11748)
  hydrogen bonds       : bond        0.04393 (  323)
  hydrogen bonds       : angle       4.38873 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 75
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7352 (t80)
REVERT: A  112 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4407 (tt)
REVERT: B  188 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8637 (mt)
  outliers start: 41
  outliers final: 23
  residues processed: 111
  average time/residue: 0.0857
  time to fit residues: 13.4076
Evaluate side-chains
  92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.150311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.112145 restraints weight = 12122.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.110963 restraints weight = 13655.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.111879 restraints weight = 15455.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.112881 restraints weight = 10734.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.113322 restraints weight = 9268.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8657  Z= 0.205
  Angle     :  0.617   8.019  11748  Z= 0.324
  Chirality :  0.044   0.165   1281
  Planarity :  0.004   0.038   1505
  Dihedral  :  6.669  51.796   1209
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.77 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 23.89 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.27), residues: 1049
  helix:  1.13 (0.28), residues: 390
  sheet: -0.97 (0.39), residues: 187
  loop : -2.31 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  69 
 TYR   0.014   0.002   TYR B 366 
 PHE   0.014   0.002   PHE A   9 
 TRP   0.016   0.001   TRP B 377 
 HIS   0.008   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8657)
  covalent geometry    : angle       0.61657 (11748)
  hydrogen bonds       : bond        0.04607 (  323)
  hydrogen bonds       : angle       4.38064 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 85
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7811 (mp10)
REVERT: A   93 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7494 (t80)
REVERT: A  112 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4371 (tt)
REVERT: A  372 LEU cc_start: 0.8662 (mt) cc_final: 0.8252 (mp)
REVERT: A  496 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6681 (tp30)
REVERT: B  188 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8601 (mt)
REVERT: B  197 MET cc_start: 0.8999 (mmp) cc_final: 0.8721 (mmm)
  outliers start: 45
  outliers final: 28
  residues processed: 122
  average time/residue: 0.0834
  time to fit residues: 14.0307
Evaluate side-chains
  104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 88 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B  45 ASN
B 339 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115650 restraints weight = 12039.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113425 restraints weight = 12025.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.114843 restraints weight = 13626.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115184 restraints weight = 9954.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115576 restraints weight = 9619.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8657  Z= 0.116
  Angle     :  0.562   9.708  11748  Z= 0.291
  Chirality :  0.041   0.164   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  6.354  50.369   1209
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.72 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 25.66 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.27), residues: 1049
  helix:  1.32 (0.28), residues: 389
  sheet: -0.79 (0.40), residues: 185
  loop : -2.22 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  69 
 TYR   0.012   0.001   TYR B 366 
 PHE   0.013   0.001   PHE A 328 
 TRP   0.010   0.001   TRP B 377 
 HIS   0.006   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8657)
  covalent geometry    : angle       0.56210 (11748)
  hydrogen bonds       : bond        0.03593 (  323)
  hydrogen bonds       : angle       4.17666 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 78
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7469 (t80)
REVERT: A  112 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4384 (tt)
REVERT: A  372 LEU cc_start: 0.8671 (mt) cc_final: 0.8256 (mp)
REVERT: A  496 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6635 (tp30)
REVERT: B  188 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8646 (mt)
REVERT: B  397 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (mt-10)
  outliers start: 37
  outliers final: 23
  residues processed: 108
  average time/residue: 0.0832
  time to fit residues: 12.4950
Evaluate side-chains
  99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  496 GLU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.153565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.114366 restraints weight = 11884.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.112040 restraints weight = 12791.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.113613 restraints weight = 13333.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.114105 restraints weight = 9581.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.114905 restraints weight = 9070.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8657  Z= 0.117
  Angle     :  0.554   8.123  11748  Z= 0.287
  Chirality :  0.041   0.156   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  6.193  52.588   1209
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.82 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.44 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.27), residues: 1049
  helix:  1.45 (0.28), residues: 388
  sheet: -0.70 (0.40), residues: 187
  loop : -2.17 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  69 
 TYR   0.011   0.001   TYR B 366 
 PHE   0.033   0.001   PHE A 391 
 TRP   0.010   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8657)
  covalent geometry    : angle       0.55410 (11748)
  hydrogen bonds       : bond        0.03475 (  323)
  hydrogen bonds       : angle       4.12582 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 83
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7505 (t80)
REVERT: A  112 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4477 (tt)
REVERT: A  372 LEU cc_start: 0.8694 (mt) cc_final: 0.8305 (mp)
REVERT: B  473 MET cc_start: 0.7650 (ppp) cc_final: 0.7309 (ppp)
  outliers start: 39
  outliers final: 24
  residues processed: 116
  average time/residue: 0.0941
  time to fit residues: 15.1035
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.154422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.116075 restraints weight = 12072.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.113388 restraints weight = 13320.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.114615 restraints weight = 14912.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115421 restraints weight = 10564.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.116100 restraints weight = 9369.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8657  Z= 0.117
  Angle     :  0.565   8.146  11748  Z= 0.290
  Chirality :  0.041   0.172   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  6.143  53.943   1209
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.82 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.66 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.27), residues: 1049
  helix:  1.44 (0.28), residues: 388
  sheet: -0.62 (0.40), residues: 185
  loop : -2.12 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  69 
 TYR   0.011   0.001   TYR B 366 
 PHE   0.012   0.001   PHE B 143 
 TRP   0.010   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8657)
  covalent geometry    : angle       0.56472 (11748)
  hydrogen bonds       : bond        0.03418 (  323)
  hydrogen bonds       : angle       4.09792 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7495 (t80)
REVERT: A  112 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4428 (tt)
REVERT: A  372 LEU cc_start: 0.8612 (mt) cc_final: 0.8231 (mp)
REVERT: A  524 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8103 (mp)
REVERT: B  397 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7680 (mt-10)
REVERT: B  473 MET cc_start: 0.7802 (ppp) cc_final: 0.7462 (ppp)
  outliers start: 39
  outliers final: 27
  residues processed: 113
  average time/residue: 0.0722
  time to fit residues: 11.8292
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  524 ILE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0030
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.155407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.116726 restraints weight = 11797.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.114368 restraints weight = 13716.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.116149 restraints weight = 15686.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116693 restraints weight = 9756.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.117337 restraints weight = 9087.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8657  Z= 0.109
  Angle     :  0.569   8.072  11748  Z= 0.290
  Chirality :  0.041   0.161   1281
  Planarity :  0.003   0.033   1505
  Dihedral  :  6.022  55.136   1209
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.15 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 26.22 %
    Favored  : 69.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.27), residues: 1049
  helix:  1.51 (0.28), residues: 388
  sheet: -0.54 (0.40), residues: 185
  loop : -2.06 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  69 
 TYR   0.011   0.001   TYR B 366 
 PHE   0.037   0.001   PHE A 391 
 TRP   0.008   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8657)
  covalent geometry    : angle       0.56865 (11748)
  hydrogen bonds       : bond        0.03171 (  323)
  hydrogen bonds       : angle       4.07019 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 82
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7555 (t80)
REVERT: A  112 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4452 (tt)
REVERT: A  372 LEU cc_start: 0.8652 (mt) cc_final: 0.8278 (mp)
REVERT: B  397 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7622 (mt-10)
REVERT: B  473 MET cc_start: 0.7828 (ppp) cc_final: 0.7612 (ppp)
  outliers start: 35
  outliers final: 26
  residues processed: 112
  average time/residue: 0.0725
  time to fit residues: 11.6568
Evaluate side-chains
  104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116184 restraints weight = 11885.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.113083 restraints weight = 13367.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.114793 restraints weight = 15177.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115539 restraints weight = 9770.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.115726 restraints weight = 9752.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8657  Z= 0.113
  Angle     :  0.569   8.212  11748  Z= 0.291
  Chirality :  0.041   0.173   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.987  55.664   1209
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.53 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 26.11 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.27), residues: 1049
  helix:  1.52 (0.28), residues: 388
  sheet: -0.54 (0.40), residues: 185
  loop : -2.04 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  69 
 TYR   0.011   0.001   TYR A 402 
 PHE   0.011   0.001   PHE A 328 
 TRP   0.009   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8657)
  covalent geometry    : angle       0.56864 (11748)
  hydrogen bonds       : bond        0.03169 (  323)
  hydrogen bonds       : angle       4.08556 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: A  112 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.4357 (tt)
REVERT: A  372 LEU cc_start: 0.8691 (mt) cc_final: 0.8309 (mp)
REVERT: B  397 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7649 (mt-10)
  outliers start: 33
  outliers final: 28
  residues processed: 107
  average time/residue: 0.0715
  time to fit residues: 10.8862
Evaluate side-chains
  105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 85 optimal weight:    0.0570
   chunk 76 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.154114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115012 restraints weight = 11876.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.112729 restraints weight = 12655.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.114436 restraints weight = 12158.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.114628 restraints weight = 9045.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.115462 restraints weight = 9118.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8657  Z= 0.112
  Angle     :  0.564   7.973  11748  Z= 0.289
  Chirality :  0.041   0.163   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.948  56.329   1209
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.06 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 26.66 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.27), residues: 1049
  helix:  1.55 (0.28), residues: 387
  sheet: -0.46 (0.40), residues: 185
  loop : -2.02 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  69 
 TYR   0.011   0.001   TYR B 366 
 PHE   0.043   0.001   PHE A 391 
 TRP   0.008   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8657)
  covalent geometry    : angle       0.56407 (11748)
  hydrogen bonds       : bond        0.03129 (  323)
  hydrogen bonds       : angle       4.04768 (  990)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7612 (t80)
REVERT: A  112 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.4347 (tt)
REVERT: A  372 LEU cc_start: 0.8733 (mt) cc_final: 0.8345 (mp)
REVERT: B  397 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7698 (mt-10)
  outliers start: 30
  outliers final: 25
  residues processed: 109
  average time/residue: 0.0681
  time to fit residues: 10.8661
Evaluate side-chains
  109 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0010
   chunk 2 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.153073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114874 restraints weight = 11914.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.113767 restraints weight = 13401.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.115163 restraints weight = 12599.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.115268 restraints weight = 9304.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.116035 restraints weight = 9389.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8657  Z= 0.115
  Angle     :  0.570   8.386  11748  Z= 0.293
  Chirality :  0.041   0.173   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.947  56.581   1209
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.44 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.77 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.27), residues: 1049
  helix:  1.55 (0.28), residues: 387
  sheet: -0.45 (0.41), residues: 185
  loop : -1.99 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  69 
 TYR   0.011   0.001   TYR B 366 
 PHE   0.010   0.001   PHE B 143 
 TRP   0.009   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8657)
  covalent geometry    : angle       0.56971 (11748)
  hydrogen bonds       : bond        0.03164 (  323)
  hydrogen bonds       : angle       4.06584 (  990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1154.39 seconds
wall clock time: 20 minutes 42.95 seconds (1242.95 seconds total)