Starting phenix.real_space_refine
on Thu Mar 13 22:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jek_36191/03_2025/8jek_36191.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.047
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: 6
    Type Number    sf(0)   Gaussians
     Fe      6      7.16       5
     P       2      5.49       5
     S      46      5.16       5
     C    5440      2.51       5
     N    1490      2.21       5
     O    1639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8623
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4167
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503}
    Chain: "B"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1080
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "C"
      Number of atoms: 3130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3130
          Classifications: {'peptide': 413}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'F3S': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 186
          Unusual residues: {'HEC': 3, 'U10': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1}
          Unresolved non-hydrogen planarities: 5

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1767  SG  CYS A 226      51.827  64.206  39.994  1.00 27.34           S
  ATOM   1738  SG  CYS A 222      50.728  68.892  44.226  1.00 28.24           S
  ATOM   1698  SG  CYS A 216      52.433  63.595  46.715  1.00 34.01           S

  Time building chain proxies: 5.45, per 1000 atoms: 0.63
  Number of scatterers: 8623
  At special positions: 0
  Unit cell: (104.4, 108.75, 77.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      6     26.01
     S      46     16.00
     P       2     15.00
     O    1639      8.00
     N    1490      7.00
     C    5440      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=11, symmetry=0
  Number of additional bonds: simple=11, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 970.6 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S A 602 "
        pdb="FE1  F3S A 602 " - pdb=" SG  CYS A 226 "
        pdb="FE4  F3S A 602 " - pdb=" SG  CYS A 216 "
        pdb="FE3  F3S A 602 " - pdb=" SG  CYS A 222 "
      Number of angles added : 9


  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      41.4% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.923A  pdb=" N   LYS A  97 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 110
      removed outlier: 3.924A  pdb=" N   THR A 108 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 124 through 130
    Processing helix  chain 'A' and resid 138 through 154
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 233 through 244
      removed outlier: 4.173A  pdb=" N   ALA A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.588A  pdb=" N   SER A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 384
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.651A  pdb=" N   LEU A 391 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASP A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 462
      removed outlier: 4.194A  pdb=" N   VAL A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 514
      removed outlier: 3.523A  pdb=" N   THR A 513 " --> pdb=" O   THR A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 541
    Processing helix  chain 'B' and resid 49 through 63
    Processing helix  chain 'B' and resid 68 through 83
    Processing helix  chain 'B' and resid 85 through 101
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.548A  pdb=" N   SER B 172 " --> pdb=" O   TYR B 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 51
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 4.313A  pdb=" N   CYS C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   HIS C  56 " --> pdb=" O   CYS C  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 51 through 56'
    Processing helix  chain 'C' and resid 95 through 106
      removed outlier: 3.518A  pdb=" N   GLY C 106 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 126
      removed outlier: 3.915A  pdb=" N   ARG C 125 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 141
    Processing helix  chain 'C' and resid 163 through 172
    Processing helix  chain 'C' and resid 185 through 197
    Processing helix  chain 'C' and resid 201 through 206
    Processing helix  chain 'C' and resid 215 through 219
      removed outlier: 3.685A  pdb=" N   TYR C 219 " --> pdb=" O   GLN C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 256
    Processing helix  chain 'C' and resid 265 through 274
    Processing helix  chain 'C' and resid 275 through 278
    Processing helix  chain 'C' and resid 279 through 291
    Processing helix  chain 'C' and resid 317 through 324
      removed outlier: 3.752A  pdb=" N   SER C 322 " --> pdb=" O   ASN C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 343
    Processing helix  chain 'C' and resid 373 through 383
    Processing helix  chain 'C' and resid 408 through 423
    Processing helix  chain 'C' and resid 431 through 440
    Processing helix  chain 'C' and resid 445 through 451
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.657A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP A   9 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   VAL A 286 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ALA A 282 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   THR A 266 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU A 258 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE A 268 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA A 256 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   PHE A 270 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   VAL A 254 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.657A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP A   9 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   VAL A 286 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   PHE A 507 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   PHE A 285 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.429A  pdb=" N   ILE A  87 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   HIS A 433 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157
    Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200
      removed outlier: 5.457A  pdb=" N   SER A 347 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   TYR A 368 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   GLY A 328 " --> pdb=" O   MET A 469 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   MET A 469 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER A 330 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ILE A 467 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73
    Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 225
    Processing sheet with id=AA8, first strand: chain 'C' and resid 384 through 388

    319 hydrogen bonds defined for protein.
    867 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: 2.22

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.76: 8764
        1.76 -     2.31: 90
        2.31 -     2.85: 0
        2.85 -     3.39: 0
        3.39 -     3.94: 3
  Bond restraints: 8857
  Sorted by residual:
  bond pdb=" S2  F3S A 602 "
       pdb="FE3  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.300  3.935 -1.635 2.00e-02 2.50e+03 6.69e+03
  bond pdb=" S4  F3S A 602 "
       pdb="FE1  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.233  3.818 -1.585 2.00e-02 2.50e+03 6.28e+03
  bond pdb=" S1  F3S A 602 "
       pdb="FE4  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.258  3.789 -1.531 2.00e-02 2.50e+03 5.86e+03
  bond pdb=" C2D HEC C 502 "
       pdb=" C3D HEC C 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.329  0.215 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C2D HEC C 503 "
       pdb=" C3D HEC C 503 "
    ideal  model  delta    sigma   weight residual
    1.544  1.333  0.211 2.00e-02 2.50e+03 1.11e+02
  ... (remaining 8852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.46: 12088
        9.46 -    18.93: 6
       18.93 -    28.39: 0
       28.39 -    37.85: 8
       37.85 -    47.31: 2
  Bond angle restraints: 12104
  Sorted by residual:
  angle pdb=" S1  F3S A 602 "
        pdb="FE4  F3S A 602 "
        pdb=" S3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     114.75   67.44   47.31 3.00e+00 1.11e-01 2.49e+02
  angle pdb=" S3  F3S A 602 "
        pdb="FE1  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     112.59   67.16   45.43 3.00e+00 1.11e-01 2.29e+02
  angle pdb=" S1  F3S A 602 "
        pdb="FE3  F3S A 602 "
        pdb=" S2  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     103.25   68.87   34.38 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" S2  F3S A 602 "
        pdb="FE3  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     103.26   69.18   34.08 3.00e+00 1.11e-01 1.29e+02
  angle pdb="FE3  F3S A 602 "
        pdb=" S2  F3S A 602 "
        pdb="FE4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
      71.75   39.22   32.53 3.00e+00 1.11e-01 1.18e+02
  ... (remaining 12099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.62: 5052
       34.62 -    69.24: 170
       69.24 -   103.86: 18
      103.86 -   138.48: 0
      138.48 -   173.09: 1
  Dihedral angle restraints: 5241
    sinusoidal: 2089
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA  PHE A  80 "
           pdb=" C   PHE A  80 "
           pdb=" N   PRO A  81 "
           pdb=" CA  PRO A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.72  -60.28     0      5.00e+00 4.00e-02 1.45e+02
  dihedral pdb=" C37 U10 C 504 "
           pdb=" C38 U10 C 504 "
           pdb=" C39 U10 C 504 "
           pdb=" C41 U10 C 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -5.63  167.47 -173.09     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C2C HEC C 502 "
           pdb=" C3C HEC C 502 "
           pdb=" CAC HEC C 502 "
           pdb=" CBC HEC C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -120.00  -38.15  -81.85     2      1.00e+01 1.00e-02 4.70e+01
  ... (remaining 5238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.462: 1276
       3.462 -    6.924: 0
       6.924 -   10.386: 0
      10.386 -   13.848: 0
      13.848 -   17.310: 1
  Chirality restraints: 1277
  Sorted by residual:
  chirality pdb=" S2  F3S A 602 "
            pdb="FE1  F3S A 602 "
            pdb="FE3  F3S A 602 "
            pdb="FE4  F3S A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -6.54   17.31 2.00e-01 2.50e+01 7.49e+03
  chirality pdb=" CB  ILE C 393 "
            pdb=" CA  ILE C 393 "
            pdb=" CG1 ILE C 393 "
            pdb=" CG2 ILE C 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" C3' FAD A 601 "
            pdb=" C2' FAD A 601 "
            pdb=" C4' FAD A 601 "
            pdb=" O3' FAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.34   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1274 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  U10 C 504 "   -0.001 2.00e-02 2.50e+03   9.06e-02 1.44e+02
        pdb=" C1M U10 C 504 "    0.063 2.00e-02 2.50e+03
        pdb=" C2  U10 C 504 "    0.028 2.00e-02 2.50e+03
        pdb=" C3  U10 C 504 "   -0.133 2.00e-02 2.50e+03
        pdb=" C4  U10 C 504 "    0.144 2.00e-02 2.50e+03
        pdb=" C5  U10 C 504 "    0.015 2.00e-02 2.50e+03
        pdb=" C6  U10 C 504 "   -0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBD HEC C 501 "   -0.033 2.00e-02 2.50e+03   6.99e-02 4.88e+01
        pdb=" CGD HEC C 501 "    0.121 2.00e-02 2.50e+03
        pdb=" O1D HEC C 501 "   -0.043 2.00e-02 2.50e+03
        pdb=" O2D HEC C 501 "   -0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  80 "   -0.101 5.00e-02 4.00e+02   1.56e-01 3.91e+01
        pdb=" N   PRO A  81 "    0.271 5.00e-02 4.00e+02
        pdb=" CA  PRO A  81 "   -0.089 5.00e-02 4.00e+02
        pdb=" CD  PRO A  81 "   -0.081 5.00e-02 4.00e+02
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 450
        2.72 -     3.27: 8576
        3.27 -     3.81: 15262
        3.81 -     4.36: 19757
        4.36 -     4.90: 32516
  Nonbonded interactions: 76561
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 397 "
            pdb=" OG  SER C 402 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" O   SER A 517 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   ARG A 358 "
            pdb=" OH  TYR A 443 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG  SER C 354 "
            pdb=" OD1 ASP C 356 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" S4  F3S A 602 "
            pdb="FE4  F3S A 602 "
     model   vdw
     2.257 2.688
  ... (remaining 76556 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.630
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
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      :  0.031   1.635   8857  Z= 1.597
  Angle     :  1.339  47.314  12104  Z= 0.518
  Chirality :  0.487  17.310   1277
  Planarity :  0.008   0.156   1572
  Dihedral  : 17.134 173.095   3229
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.21 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.25), residues: 1083
  helix:  1.47 (0.28), residues: 363
  sheet:  0.37 (0.64), residues: 72
  loop : -0.70 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 111 
 HIS   0.006   0.001   HIS A 110 
 PHE   0.017   0.001   PHE A 270 
 TYR   0.014   0.001   TYR A  79 
 ARG   0.002   0.000   ARG C 125 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  505 ASN cc_start: 0.7804 (t0) cc_final: 0.7253 (t0)
REVERT: C  315 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5098 (p90)
  outliers start: 15
  outliers final: 13
  residues processed: 117
  average time/residue: 1.3230
  time to fit residues: 166.6138
Evaluate side-chains
  118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  445 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.132035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.103343 restraints weight = 9007.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.55
r_work: 0.2998 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.0721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.192   8857  Z= 0.324
  Angle     :  1.323  68.843  12104  Z= 0.491
  Chirality :  0.099   3.152   1277
  Planarity :  0.006   0.111   1572
  Dihedral  : 12.304 153.495   1318
  Min Nonbonded Distance : 1.477

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.71 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.74 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1083
  helix:  1.51 (0.27), residues: 387
  sheet:  0.38 (0.64), residues: 73
  loop : -0.67 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 111 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.015   0.001   PHE A 270 
 TYR   0.016   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 205 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 ASN cc_start: 0.8720 (m110) cc_final: 0.8429 (m110)
REVERT: A  478 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7012 (p-80)
REVERT: C  135 TYR cc_start: 0.8340 (t80) cc_final: 0.8085 (t80)
REVERT: C  143 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6984 (pttp)
  outliers start: 24
  outliers final: 10
  residues processed: 121
  average time/residue: 1.1003
  time to fit residues: 143.9846
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 81 optimal weight:    7.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.098464 restraints weight = 9342.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.54
r_work: 0.2971 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.0907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.091   8857  Z= 0.446
  Angle     :  1.164  88.253  12104  Z= 0.464
  Chirality :  0.062   1.164   1277
  Planarity :  0.006   0.107   1572
  Dihedral  : 12.353 150.515   1309
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.36 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.21 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.99 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.25), residues: 1083
  helix:  1.22 (0.26), residues: 385
  sheet:  0.08 (0.63), residues: 76
  loop : -0.80 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 173 
 HIS   0.007   0.001   HIS C 200 
 PHE   0.022   0.002   PHE A  80 
 TYR   0.021   0.002   TYR A  79 
 ARG   0.003   0.000   ARG A  52 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  478 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7296 (p-80)
REVERT: A  539 ASN cc_start: 0.8414 (t0) cc_final: 0.8065 (t0)
REVERT: C  135 TYR cc_start: 0.8367 (t80) cc_final: 0.8150 (t80)
REVERT: C  143 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7056 (pttp)
  outliers start: 27
  outliers final: 16
  residues processed: 121
  average time/residue: 1.4654
  time to fit residues: 191.1906
Evaluate side-chains
  125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
A 505 ASN
C 326 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.133710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.107596 restraints weight = 8798.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.22
r_work: 0.3067 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   8857  Z= 0.260
  Angle     :  1.058  83.219  12104  Z= 0.414
  Chirality :  0.061   1.421   1277
  Planarity :  0.006   0.099   1572
  Dihedral  : 11.890 146.686   1308
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.11 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1083
  helix:  1.48 (0.27), residues: 387
  sheet:  0.24 (0.63), residues: 73
  loop : -0.70 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 111 
 HIS   0.004   0.001   HIS C 200 
 PHE   0.016   0.001   PHE A  80 
 TYR   0.018   0.001   TYR A  79 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 ASN cc_start: 0.8887 (m110) cc_final: 0.8633 (m110)
REVERT: A  478 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7279 (p-80)
REVERT: A  539 ASN cc_start: 0.8525 (t0) cc_final: 0.8197 (t0)
REVERT: C  143 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7133 (pttp)
  outliers start: 24
  outliers final: 15
  residues processed: 120
  average time/residue: 1.0465
  time to fit residues: 135.5696
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0050
   chunk 7 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.137498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.112357 restraints weight = 8742.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.18
r_work: 0.3097 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8857  Z= 0.217
  Angle     :  1.032  82.394  12104  Z= 0.398
  Chirality :  0.061   1.464   1277
  Planarity :  0.005   0.098   1572
  Dihedral  : 11.497 137.595   1308
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.22 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1083
  helix:  1.60 (0.27), residues: 393
  sheet:  0.39 (0.64), residues: 71
  loop : -0.56 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 111 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.014   0.001   PHE A 270 
 TYR   0.015   0.001   TYR A  79 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 ASN cc_start: 0.8842 (m110) cc_final: 0.8635 (m110)
REVERT: A  478 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7090 (p-80)
REVERT: A  539 ASN cc_start: 0.8470 (t0) cc_final: 0.8165 (t0)
REVERT: B  112 MET cc_start: 0.8305 (ttp) cc_final: 0.8094 (ttp)
REVERT: B  126 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7115 (mtp180)
REVERT: C  135 TYR cc_start: 0.8636 (t80) cc_final: 0.8421 (t80)
REVERT: C  143 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7146 (pttp)
REVERT: C  315 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.5780 (p90)
  outliers start: 26
  outliers final: 14
  residues processed: 118
  average time/residue: 1.1094
  time to fit residues: 141.1144
Evaluate side-chains
  123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 59 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.136261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.110814 restraints weight = 8692.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.17
r_work: 0.3085 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8857  Z= 0.241
  Angle     :  1.043  82.386  12104  Z= 0.403
  Chirality :  0.061   1.462   1277
  Planarity :  0.005   0.091   1572
  Dihedral  : 11.417 131.422   1308
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.71 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.54 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1083
  helix:  1.63 (0.27), residues: 393
  sheet:  0.42 (0.64), residues: 71
  loop : -0.53 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 173 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.016   0.001   PHE A 270 
 TYR   0.018   0.001   TYR A  79 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7780 (m-30)
REVERT: A  478 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7191 (p-80)
REVERT: A  539 ASN cc_start: 0.8481 (t0) cc_final: 0.8168 (t0)
REVERT: B  112 MET cc_start: 0.8338 (ttp) cc_final: 0.8121 (ttp)
REVERT: B  126 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7195 (mtp85)
REVERT: C  143 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7115 (pttp)
  outliers start: 26
  outliers final: 16
  residues processed: 121
  average time/residue: 1.0480
  time to fit residues: 136.7601
Evaluate side-chains
  121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.111471 restraints weight = 8797.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.19
r_work: 0.3094 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8857  Z= 0.227
  Angle     :  1.040  82.379  12104  Z= 0.402
  Chirality :  0.061   1.464   1277
  Planarity :  0.005   0.085   1572
  Dihedral  : 11.284 125.187   1308
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.88 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 1083
  helix:  1.68 (0.27), residues: 393
  sheet:  0.41 (0.65), residues: 71
  loop : -0.50 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 111 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.015   0.001   PHE A 270 
 TYR   0.016   0.001   TYR A  79 
 ARG   0.001   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7776 (m-30)
REVERT: A  460 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (tmtm)
REVERT: A  478 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7127 (p-80)
REVERT: A  539 ASN cc_start: 0.8502 (t0) cc_final: 0.8189 (t0)
REVERT: B  112 MET cc_start: 0.8329 (ttp) cc_final: 0.8110 (ttp)
REVERT: B  126 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7147 (mtp85)
REVERT: C  143 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7138 (pttp)
  outliers start: 27
  outliers final: 17
  residues processed: 114
  average time/residue: 1.0456
  time to fit residues: 129.0454
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 102 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.136309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.110689 restraints weight = 8860.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.20
r_work: 0.3083 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   8857  Z= 0.243
  Angle     :  1.051  82.282  12104  Z= 0.408
  Chirality :  0.062   1.469   1277
  Planarity :  0.005   0.084   1572
  Dihedral  : 11.223 117.970   1308
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.71 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.45 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1083
  helix:  1.67 (0.27), residues: 393
  sheet:  0.47 (0.65), residues: 71
  loop : -0.52 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 128 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.017   0.001   PHE A 270 
 TYR   0.018   0.001   TYR A  79 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7772 (m-30)
REVERT: A  460 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7745 (tmtm)
REVERT: A  478 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7184 (p-80)
REVERT: A  539 ASN cc_start: 0.8503 (t0) cc_final: 0.8188 (t0)
REVERT: B  112 MET cc_start: 0.8342 (ttp) cc_final: 0.8118 (ttp)
REVERT: B  126 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7154 (mtp180)
REVERT: C  143 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7105 (pttp)
  outliers start: 24
  outliers final: 17
  residues processed: 110
  average time/residue: 1.0773
  time to fit residues: 127.7747
Evaluate side-chains
  120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  460 LYS
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.133725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.107981 restraints weight = 8866.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.20
r_work: 0.3035 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   8857  Z= 0.306
  Angle     :  1.079  81.836  12104  Z= 0.423
  Chirality :  0.064   1.482   1277
  Planarity :  0.005   0.086   1572
  Dihedral  : 11.408 118.268   1308
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.17 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.56 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1083
  helix:  1.55 (0.27), residues: 392
  sheet:  0.35 (0.64), residues: 73
  loop : -0.59 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 128 
 HIS   0.005   0.001   HIS C 200 
 PHE   0.020   0.002   PHE A 270 
 TYR   0.021   0.002   TYR A  79 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7253 (p-80)
REVERT: A  539 ASN cc_start: 0.8537 (t0) cc_final: 0.8209 (t0)
REVERT: B  112 MET cc_start: 0.8378 (ttp) cc_final: 0.8155 (ttp)
REVERT: C  143 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7091 (pttp)
  outliers start: 24
  outliers final: 18
  residues processed: 114
  average time/residue: 0.9733
  time to fit residues: 120.4559
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.0030
   chunk 30 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0170
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6032

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.137246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.111738 restraints weight = 8824.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.19
r_work: 0.3109 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   8857  Z= 0.221
  Angle     :  1.046  82.256  12104  Z= 0.403
  Chirality :  0.061   1.469   1277
  Planarity :  0.005   0.112   1572
  Dihedral  : 11.079 111.002   1308
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.46 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1083
  helix:  1.68 (0.27), residues: 393
  sheet:  0.49 (0.65), residues: 71
  loop : -0.50 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.017   0.001   PHE A 270 
 TYR   0.014   0.001   TYR A 443 
 ARG   0.002   0.000   ARG C 323 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7750 (m-30)
REVERT: A  478 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7070 (p-80)
REVERT: A  539 ASN cc_start: 0.8517 (t0) cc_final: 0.8209 (t0)
REVERT: B  112 MET cc_start: 0.8319 (ttp) cc_final: 0.8096 (ttp)
REVERT: B  126 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7156 (mtp180)
REVERT: C  143 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7082 (pttp)
REVERT: C  315 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5648 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 111
  average time/residue: 1.0703
  time to fit residues: 128.6988
Evaluate side-chains
  120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  143 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  267 MET
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  429 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 102 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.133902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.107981 restraints weight = 8857.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.18
r_work: 0.3062 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   8857  Z= 0.322
  Angle     :  1.084  81.751  12104  Z= 0.427
  Chirality :  0.063   1.484   1277
  Planarity :  0.006   0.116   1572
  Dihedral  : 11.522 114.019   1306
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.26 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.35 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1083
  helix:  1.52 (0.27), residues: 391
  sheet:  0.41 (0.64), residues: 73
  loop : -0.60 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 128 
 HIS   0.005   0.001   HIS C 200 
 PHE   0.020   0.002   PHE A  80 
 TYR   0.019   0.002   TYR A  79 
 ARG   0.002   0.000   ARG C 386 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6413.70 seconds
wall clock time: 113 minutes 52.74 seconds (6832.74 seconds total)