Starting phenix.real_space_refine
on Fri Sep 11 02:52:34 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ybv_10774/09_2026/6ybv_10774.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic.
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      77      5.49       5
     S      21      5.16       5
     C    3877      2.51       5
     N    1250      2.21       5
     O    1506      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6731
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "s"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1123
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "r"
      Number of atoms: 2215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2215
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 9, 'TRANS': 265}
    Chain: "w"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1604
          Classifications: {'RNAv2': 75}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 12, 'rna3p': 62}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "k"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Classifications: {'RNAv2': 3}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2}
          Link IDs: {'rna3p': 2}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'  A%rna3p_pur:plan': 2, '  A%rna3p_pur:plan2': 2, '  A%rna2p_pur:plan': 1, '  A%rna2p_pur:plan2': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "t"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 356, 1750
          Classifications: {'peptide': 356}
          Incomplete info: {'truncation_to_alanine': 298}
          Link IDs: {'PTRANS': 15, 'TRANS': 340}
          Chain breaks: 4
          Unresolved chain link angles: 15
          Unresolved non-hydrogen bonds: 1009
          Unresolved non-hydrogen angles: 1285
          Unresolved non-hydrogen dihedrals: 814
          Unresolved non-hydrogen chiralities: 125
          Planarities with less than four sites: {'GLU:plan': 23, 'ARG:plan': 17, 'GLN:plan1': 13, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 8, 'TYR:plan': 6, 'ASP:plan': 9, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 445
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ALA t  51 " occ=0.32
      ... (3 atoms not shown)
      pdb=" CB  ALA t  51 " occ=0.32
    residue:
      pdb=" N   GLN t 206 " occ=0.55
      ... (3 atoms not shown)
      pdb=" CB  GLN t 206 " occ=0.55
    residue:
      pdb=" N   LEU t 208 " occ=0.35
      ... (3 atoms not shown)
      pdb=" CB  LEU t 208 " occ=0.35
    residue:
      pdb=" N   ASN t 431 " occ=0.42
      ... (3 atoms not shown)
      pdb=" CB  ASN t 431 " occ=0.42
  Time building chain proxies: 1.76, per 1000 atoms: 0.26
  Number of scatterers: 6731
  At special positions: 0
  Unit cell: (111.696, 117.066, 106.326, 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      21     16.00
     P      77     15.00
     O    1506      8.00
     N    1250      7.00
     C    3877      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: 0.45
  Conformation dependent library (CDL) restraints added in 274.3 milliseconds
  

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      33.7% alpha, 16.4% beta
      14 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 's' and resid 176 through 186
    Processing helix  chain 's' and resid 221 through 229
    Processing helix  chain 's' and resid 234 through 243
      removed outlier: 4.012A  pdb=" N   ALA s 238 " --> pdb=" O   LYS s 234 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE s 239 " --> pdb=" O   HIS s 235 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 244 through 246
      No H-bonds generated for 'chain 's' and resid 244 through 246'
    Processing helix  chain 's' and resid 263 through 278
    Processing helix  chain 'r' and resid 58 through 63
      removed outlier: 3.609A  pdb=" N   LEU r  62 " --> pdb=" O   SER r  58 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 91 through 119
    Processing helix  chain 'r' and resid 123 through 134
    Processing helix  chain 'r' and resid 134 through 142
    Processing helix  chain 'r' and resid 146 through 157
    Processing helix  chain 'r' and resid 161 through 166
      removed outlier: 3.694A  pdb=" N   LEU r 166 " --> pdb=" O   LEU r 163 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 169 through 181
      removed outlier: 3.697A  pdb=" N   ARG r 173 " --> pdb=" O   ASN r 169 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU r 174 " --> pdb=" O   GLU r 170 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 203 through 218
    Processing helix  chain 'r' and resid 243 through 262
      removed outlier: 3.720A  pdb=" N   GLY r 247 " --> pdb=" O   GLU r 243 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER r 249 " --> pdb=" O   THR r 245 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 53 through 63
    Processing helix  chain 't' and resid 69 through 76
    Processing helix  chain 't' and resid 141 through 152
      removed outlier: 3.949A  pdb=" N   MET t 145 " --> pdb=" O   LEU t 141 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL t 151 " --> pdb=" O   ASN t 147 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 168 through 181
    Processing helix  chain 't' and resid 196 through 212
    Processing helix  chain 't' and resid 214 through 219
      removed outlier: 4.131A  pdb=" N   GLY t 218 " --> pdb=" O   VAL t 215 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 231 through 243
    Processing helix  chain 't' and resid 344 through 349
    Processing sheet with id=AA1, first strand: chain 's' and resid 218 through 219
      removed outlier: 4.107A  pdb=" N   VAL s 257 " --> pdb=" O   SER s 249 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER s 249 " --> pdb=" O   VAL s 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 's' and resid 291 through 293
      removed outlier: 3.693A  pdb=" N   GLN s 292 " --> pdb=" O   PHE s 299 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE s 299 " --> pdb=" O   GLN s 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'r' and resid 19 through 24
      removed outlier: 8.870A  pdb=" N   LEU r  85 " --> pdb=" O   GLU r  43 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   MET r  45 " --> pdb=" O   LEU r  85 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ASP r  84 " --> pdb=" O   ILE r  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'r' and resid 226 through 229
      removed outlier: 3.751A  pdb=" N   ASN r 228 " --> pdb=" O   VAL r 236 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU r 196 " --> pdb=" O   ASN r 270 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN r 270 " --> pdb=" O   GLU r 196 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 't' and resid 84 through 86
      removed outlier: 3.615A  pdb=" N   ALA t  84 " --> pdb=" O   PHE t 132 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ILE t  44 " --> pdb=" O   VAL t 133 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   GLY t  45 " --> pdb=" O   LEU t 156 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU t 158 " --> pdb=" O   GLY t  45 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   ILE t  47 " --> pdb=" O   LEU t 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ALA t 155 " --> pdb=" O   LEU t 186 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   LEU t 188 " --> pdb=" O   ALA t 155 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU t 157 " --> pdb=" O   LEU t 188 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE t 222 " --> pdb=" O   ILE t 187 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 't' and resid 283 through 285
      removed outlier: 6.429A  pdb=" N   ARG t 255 " --> pdb=" O   LEU t 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 't' and resid 279 through 281
      removed outlier: 3.777A  pdb=" N   ALA t 279 " --> pdb=" O   VAL t 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 't' and resid 367 through 368
      removed outlier: 3.908A  pdb=" N   VAL t 433 " --> pdb=" O   PHE t 368 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 't' and resid 411 through 413
      removed outlier: 3.756A  pdb=" N   ASN t 407 " --> pdb=" O   ALA t 442 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ALA t 442 " --> pdb=" O   ASN t 407 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE t 441 " --> pdb=" O   TRP t 456 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   TRP t 456 " --> pdb=" O   ILE t 441 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU t 443 " --> pdb=" O   ILE t 454 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TRP t 456 " --> pdb=" O   PHE t 376 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE t 373 " --> pdb=" O   GLY t 425 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY t 425 " --> pdb=" O   ILE t 373 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU t 424 " --> pdb=" O   VAL t 420 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   VAL t 420 " --> pdb=" O   LEU t 424 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   LYS t 426 " --> pdb=" O   SER t 418 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER t 418 " --> pdb=" O   LYS t 426 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL t 428 " --> pdb=" O   ARG t 416 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    624 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1471
        1.33 -     1.45: 1866
        1.45 -     1.57: 3452
        1.57 -     1.70: 150
        1.70 -     1.82: 31
  Bond restraints: 6970
  Sorted by residual:
  bond pdb=" C   VAL r  90 "
       pdb=" N   SER r  91 "
    ideal  model  delta    sigma   weight residual
    1.339  1.213  0.126 5.57e-02 3.22e+02 5.13e+00
  bond pdb=" C   CYS t 311 "
       pdb=" N   LYS t 312 "
    ideal  model  delta    sigma   weight residual
    1.335  1.256  0.079 3.59e-02 7.76e+02 4.81e+00
  bond pdb=" N   GLU t 324 "
       pdb=" CA  GLU t 324 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.64e+00
  bond pdb=" CB  VAL r  71 "
       pdb=" CG2 VAL r  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  bond pdb=" CB  ARG r  88 "
       pdb=" CG  ARG r  88 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.056 3.00e-02 1.11e+03 3.45e+00
  ... (remaining 6965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 9204
        3.00 -     6.01: 580
        6.01 -     9.01: 45
        9.01 -    12.01: 6
       12.01 -    15.02: 5
  Bond angle restraints: 9840
  Sorted by residual:
  angle pdb=" N   PRO t 168 "
        pdb=" CA  PRO t 168 "
        pdb=" C   PRO t 168 "
      ideal   model   delta    sigma   weight residual
     112.47  124.78  -12.31 2.06e+00 2.36e-01 3.57e+01
  angle pdb=" N   VAL s 203 "
        pdb=" CA  VAL s 203 "
        pdb=" C   VAL s 203 "
      ideal   model   delta    sigma   weight residual
     109.34   97.09   12.25 2.08e+00 2.31e-01 3.47e+01
  angle pdb=" N   GLY s 252 "
        pdb=" CA  GLY s 252 "
        pdb=" C   GLY s 252 "
      ideal   model   delta    sigma   weight residual
     112.18  105.50    6.68 1.34e+00 5.57e-01 2.48e+01
  angle pdb=" CA  ARG s 272 "
        pdb=" CB  ARG s 272 "
        pdb=" CG  ARG s 272 "
      ideal   model   delta    sigma   weight residual
     114.10  124.02   -9.92 2.00e+00 2.50e-01 2.46e+01
  angle pdb=" C   MET t 180 "
        pdb=" N   LYS t 181 "
        pdb=" CA  LYS t 181 "
      ideal   model   delta    sigma   weight residual
     121.54  130.66   -9.12 1.91e+00 2.74e-01 2.28e+01
  ... (remaining 9835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 3291
       16.23 -    32.45: 419
       32.45 -    48.68: 205
       48.68 -    64.91: 106
       64.91 -    81.14: 21
  Dihedral angle restraints: 4042
    sinusoidal: 1820
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" C4'   C w  73 "
           pdb=" C3'   C w  73 "
           pdb=" C2'   C w  73 "
           pdb=" C1'   C w  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -42.79   79.14     1      3.10e+00 1.04e-01 8.11e+02
  dihedral pdb=" C4'   U w   8 "
           pdb=" C3'   U w   8 "
           pdb=" C2'   U w   8 "
           pdb=" C1'   U w   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -41.95   78.29     1      3.10e+00 1.04e-01 7.96e+02
  dihedral pdb=" C4'   A w  57 "
           pdb=" C3'   A w  57 "
           pdb=" C2'   A w  57 "
           pdb=" C1'   A w  57 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.56   73.91     1      3.10e+00 1.04e-01 7.22e+02
  ... (remaining 4039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 825
       0.075 -    0.149: 261
       0.149 -    0.224: 74
       0.224 -    0.299: 63
       0.299 -    0.374: 12
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" C3'   C w  73 "
            pdb=" C4'   C w  73 "
            pdb=" O3'   C w  73 "
            pdb=" C2'   C w  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.87    0.37 2.00e-01 2.50e+01 3.49e+00
  chirality pdb=" C3'   U w   8 "
            pdb=" C4'   U w   8 "
            pdb=" O3'   U w   8 "
            pdb=" C2'   U w   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.86    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" C1'   C w  73 "
            pdb=" O4'   C w  73 "
            pdb=" C2'   C w  73 "
            pdb=" N1    C w  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.11    0.35 2.00e-01 2.50e+01 3.07e+00
  ... (remaining 1232 not shown)

  Planarity restraints: 1011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN s 292 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" CD  GLN s 292 "    0.063 2.00e-02 2.50e+03
        pdb=" OE1 GLN s 292 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 GLN s 292 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G w  12 "   -0.008 2.00e-02 2.50e+03   2.03e-02 1.24e+01
        pdb=" N9    G w  12 "    0.037 2.00e-02 2.50e+03
        pdb=" C8    G w  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G w  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    G w  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G w  12 "    0.009 2.00e-02 2.50e+03
        pdb=" O6    G w  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G w  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G w  12 "    0.033 2.00e-02 2.50e+03
        pdb=" N2    G w  12 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3    G w  12 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G w  12 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA t 323 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   ALA t 323 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ALA t 323 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU t 324 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1008 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 888
        2.74 -     3.28: 6205
        3.28 -     3.82: 11334
        3.82 -     4.36: 12440
        4.36 -     4.90: 19659
  Nonbonded interactions: 50526
  Sorted by model distance:
  nonbonded pdb=" O6    G w   9 "
            pdb=" O2'   A w  19 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ALA s 196 "
            pdb=" NH2 ARG s 285 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OG1 THR s 246 "
            pdb=" O   LYS s 259 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR r 220 "
            pdb=" O   MET r 223 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LYS r 104 "
            pdb=" OG1 THR r 107 "
     model   vdw
     2.277 3.040
  ... (remaining 50521 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.32 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:             14.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.930
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5584
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.126   6970  Z= 0.418
  Angle     :  1.547  15.017   9840  Z= 0.815
  Chirality :  0.099   0.374   1235
  Planarity :  0.009   0.069   1011
  Dihedral  : 20.398  81.135   2598
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.09 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 22.67 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.26), residues: 755
  helix: -0.78 (0.32), residues: 214
  sheet:  0.05 (0.50), residues: 109
  loop : -2.41 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG s 285 
 TYR   0.030   0.004   TYR s 176 
 PHE   0.032   0.005   PHE r 131 
 TRP   0.009   0.004   TRP r 136 
 HIS   0.007   0.003   HIS r 155 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00852 /  0.42 ( 6970)
  covalent geometry    : angle       1.54675 /  0.82 ( 9840)
  hydrogen bonds       : bond        0.24647 / 15.58 (  253)
  hydrogen bonds       : angle       9.06598 /  6.52 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: r   74 ILE cc_start: 0.7523 (mm) cc_final: 0.7291 (mm)
REVERT: r   89 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4586 (mmt180)
REVERT: r  121 TYR cc_start: 0.2630 (OUTLIER) cc_final: 0.1330 (m-80)
REVERT: r  182 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6591 (ttp-170)
REVERT: r  273 MET cc_start: 0.3051 (mtt) cc_final: 0.0830 (ttt)
  outliers start: 25
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1088
  time to fit residues: 16.1405
Evaluate side-chains
  62 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  121 TYR
Chi-restraints excluded: chain r residue  271 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
s 181 ASN
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 306 HIS
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r 179 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.113799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.106474 restraints weight = 41772.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.107072 restraints weight = 35700.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.108142 restraints weight = 25804.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.108090 restraints weight = 21573.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.108272 restraints weight = 16753.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4185 r_free = 0.4185    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4181 r_free = 0.4181    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (14 function evaluations)
r_final: 0.4181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5919
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.136   6970  Z= 0.384
  Angle     :  1.361  12.719   9840  Z= 0.601
  Chirality :  0.089   0.727   1235
  Planarity :  0.007   0.077   1011
  Dihedral  : 17.844 163.476   1751
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 22.89
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.23 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 31.20 %
    Favored  : 63.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.27), residues: 755
  helix: -0.77 (0.30), residues: 219
  sheet: -0.38 (0.46), residues: 116
  loop : -2.40 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG r 234 
 TYR   0.023   0.003   TYR r  82 
 PHE   0.016   0.003   PHE s 239 
 TRP   0.012   0.003   TRP r 136 
 HIS   0.016   0.003   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00794 /  0.38 ( 6970)
  covalent geometry    : angle       1.36092 /  0.60 ( 9840)
  hydrogen bonds       : bond        0.08863 /  5.32 (  253)
  hydrogen bonds       : angle       7.10697 /  4.88 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: s  264 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7077 (tt0)
REVERT: r   48 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8548 (tm)
REVERT: r   89 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.5640 (mmt180)
REVERT: r  182 ARG cc_start: 0.7409 (mtm180) cc_final: 0.6866 (ttp80)
  outliers start: 21
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0903
  time to fit residues: 9.4287
Evaluate side-chains
  57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  264 GLN
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   27 ILE
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  121 TYR
Chi-restraints excluded: chain r residue  278 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r  40 ASN
r 179 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.112740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.105194 restraints weight = 40110.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.105415 restraints weight = 39732.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.106637 restraints weight = 30004.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.106483 restraints weight = 21841.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.106806 restraints weight = 19786.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4155 r_free = 0.4155    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4155 r_free = 0.4155    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6022
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090   6970  Z= 0.341
  Angle     :  1.196  17.466   9840  Z= 0.531
  Chirality :  0.079   0.753   1235
  Planarity :  0.006   0.065   1011
  Dihedral  : 18.267 176.717   1748
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 22.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.27 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 30.93 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.27), residues: 755
  helix: -1.03 (0.30), residues: 223
  sheet: -1.45 (0.51), residues: 97
  loop : -2.58 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG s 231 
 TYR   0.026   0.003   TYR r  82 
 PHE   0.022   0.003   PHE s 239 
 TRP   0.008   0.002   TRP r 136 
 HIS   0.006   0.002   HIS s 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00701 /  0.34 ( 6970)
  covalent geometry    : angle       1.19620 /  0.53 ( 9840)
  hydrogen bonds       : bond        0.08462 /  5.21 (  253)
  hydrogen bonds       : angle       6.86869 /  4.69 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 0.217 
Fit side-chains
REVERT: s  226 CYS cc_start: 0.6020 (t) cc_final: 0.5176 (t)
REVERT: s  264 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7237 (tm-30)
REVERT: r   89 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.5811 (mmt180)
  outliers start: 27
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0862
  time to fit residues: 8.7195
Evaluate side-chains
  57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  264 GLN
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   71 VAL
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  242 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   chunk 64 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 179 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 = 0.4320 r_free = 0.4320 target = 0.115322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.107884 restraints weight = 41392.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.108072 restraints weight = 41119.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.109128 restraints weight = 30652.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.109105 restraints weight = 26501.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.109680 restraints weight = 19795.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4213 r_free = 0.4213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4213 r_free = 0.4213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6970  Z= 0.179
  Angle     :  0.929   9.146   9840  Z= 0.414
  Chirality :  0.069   0.645   1235
  Planarity :  0.005   0.051   1011
  Dihedral  : 17.756 179.202   1744
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.96 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 30.67 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.28), residues: 755
  helix: -0.33 (0.32), residues: 223
  sheet: -1.58 (0.49), residues: 91
  loop : -2.30 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG s 296 
 TYR   0.017   0.002   TYR r 150 
 PHE   0.015   0.002   PHE s 239 
 TRP   0.004   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 ( 6970)
  covalent geometry    : angle       0.92902 /  0.41 ( 9840)
  hydrogen bonds       : bond        0.07244 /  4.55 (  253)
  hydrogen bonds       : angle       5.94946 /  4.02 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.139 
Fit side-chains
REVERT: s  204 MET cc_start: 0.4020 (pmm) cc_final: 0.2642 (pmm)
REVERT: s  226 CYS cc_start: 0.5195 (t) cc_final: 0.4915 (t)
REVERT: r   30 MET cc_start: 0.5543 (ptt) cc_final: 0.5241 (ptm)
REVERT: r   89 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.5570 (mmt180)
REVERT: r  220 THR cc_start: 0.4163 (OUTLIER) cc_final: 0.3860 (m)
  outliers start: 24
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0884
  time to fit residues: 8.3081
Evaluate side-chains
  55 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  229 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 31 optimal weight:    0.4980
   chunk 63 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 68 optimal weight:   30.0000
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
s 221 ASN
s 301 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.114872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.107299 restraints weight = 41659.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.107326 restraints weight = 38717.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.107550 restraints weight = 34787.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.107734 restraints weight = 30229.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.107823 restraints weight = 28822.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4180 r_free = 0.4180    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4180 r_free = 0.4180    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5879
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6970  Z= 0.176
  Angle     :  0.905  11.593   9840  Z= 0.398
  Chirality :  0.066   0.620   1235
  Planarity :  0.005   0.049   1011
  Dihedral  : 17.584 177.407   1744
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.34 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 31.20 %
    Favored  : 63.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.28), residues: 755
  helix: -0.10 (0.32), residues: 223
  sheet: -1.63 (0.50), residues: 94
  loop : -2.09 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG s 296 
 TYR   0.014   0.002   TYR r  82 
 PHE   0.018   0.002   PHE s 239 
 TRP   0.003   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.18 ( 6970)
  covalent geometry    : angle       0.90497 /  0.40 ( 9840)
  hydrogen bonds       : bond        0.07026 /  4.31 (  253)
  hydrogen bonds       : angle       5.78566 /  3.93 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.166 
Fit side-chains
REVERT: s  204 MET cc_start: 0.3939 (pmm) cc_final: 0.3066 (pmm)
REVERT: s  226 CYS cc_start: 0.5298 (t) cc_final: 0.4883 (t)
REVERT: r   30 MET cc_start: 0.6183 (ptt) cc_final: 0.5917 (ptm)
REVERT: r   89 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.5665 (mmt180)
REVERT: r  220 THR cc_start: 0.4542 (OUTLIER) cc_final: 0.4239 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 67
  average time/residue: 0.0677
  time to fit residues: 6.3471
Evaluate side-chains
  56 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  229 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0050
   overall best weight:    0.9796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
s 301 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.117340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.109587 restraints weight = 41766.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.110551 restraints weight = 28685.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.111153 restraints weight = 21574.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.111624 restraints weight = 17677.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.111810 restraints weight = 14984.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4244 r_free = 0.4244    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4244 r_free = 0.4244    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5776
moved from start:          0.5340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6970  Z= 0.139
  Angle     :  0.817   8.579   9840  Z= 0.361
  Chirality :  0.062   0.589   1235
  Planarity :  0.004   0.056   1011
  Dihedral  : 17.289 177.336   1744
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.83 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 32.53 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.29), residues: 755
  helix:  0.47 (0.33), residues: 223
  sheet: -1.49 (0.48), residues: 104
  loop : -1.94 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG r 244 
 TYR   0.016   0.002   TYR s 274 
 PHE   0.009   0.001   PHE s 299 
 TRP   0.007   0.002   TRP r 136 
 HIS   0.004   0.001   HIS s 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.14 ( 6970)
  covalent geometry    : angle       0.81718 /  0.36 ( 9840)
  hydrogen bonds       : bond        0.06756 /  4.33 (  253)
  hydrogen bonds       : angle       5.33415 /  3.64 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.218 
Fit side-chains
REVERT: r   30 MET cc_start: 0.5703 (ptt) cc_final: 0.5481 (ptm)
REVERT: r   89 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.5539 (mmt180)
REVERT: r  179 ASN cc_start: 0.6624 (p0) cc_final: 0.6073 (p0)
REVERT: r  220 THR cc_start: 0.4803 (OUTLIER) cc_final: 0.4486 (m)
  outliers start: 15
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0712
  time to fit residues: 6.5625
Evaluate side-chains
  54 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  220 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
s 301 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.114479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.107051 restraints weight = 41215.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.106969 restraints weight = 41751.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.108056 restraints weight = 34846.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.107922 restraints weight = 26429.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.108122 restraints weight = 23068.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4179 r_free = 0.4179    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4179 r_free = 0.4179    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (11 function evaluations)
r_final: 0.4179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6970  Z= 0.218
  Angle     :  0.947  13.433   9840  Z= 0.417
  Chirality :  0.065   0.627   1235
  Planarity :  0.005   0.056   1011
  Dihedral  : 17.602 179.813   1742
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.93 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 31.73 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.29), residues: 755
  helix: -0.17 (0.32), residues: 222
  sheet: -1.57 (0.54), residues: 84
  loop : -2.00 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG r 113 
 TYR   0.017   0.002   TYR r 150 
 PHE   0.024   0.002   PHE s 239 
 TRP   0.010   0.002   TRP r 136 
 HIS   0.004   0.001   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00457 /  0.22 ( 6970)
  covalent geometry    : angle       0.94710 /  0.42 ( 9840)
  hydrogen bonds       : bond        0.07117 /  4.35 (  253)
  hydrogen bonds       : angle       5.83583 /  3.98 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.225 
Fit side-chains
REVERT: r   30 MET cc_start: 0.6258 (ptt) cc_final: 0.6025 (ptm)
REVERT: r   89 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.5830 (mmt180)
REVERT: r  242 LEU cc_start: 0.6844 (pt) cc_final: 0.6408 (mp)
REVERT: r  255 MET cc_start: 0.5173 (mmm) cc_final: 0.4877 (mpp)
  outliers start: 20
  outliers final: 14
  residues processed: 62
  average time/residue: 0.0698
  time to fit residues: 6.1731
Evaluate side-chains
  58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  229 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    0.1980
   chunk 46 optimal weight:    7.9990
   chunk 70 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 68 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.5386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.114377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.106487 restraints weight = 41256.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.107462 restraints weight = 28449.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.108139 restraints weight = 21475.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.108543 restraints weight = 17356.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.108852 restraints weight = 14902.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4186 r_free = 0.4186    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4186 r_free = 0.4186    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5922
moved from start:          0.5912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6970  Z= 0.212
  Angle     :  0.950  11.700   9840  Z= 0.419
  Chirality :  0.065   0.633   1235
  Planarity :  0.005   0.059   1011
  Dihedral  : 17.725 177.336   1742
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.48 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 32.53 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.29), residues: 755
  helix: -0.25 (0.32), residues: 222
  sheet: -1.87 (0.49), residues: 102
  loop : -2.03 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG s 296 
 TYR   0.013   0.002   TYR s 278 
 PHE   0.017   0.002   PHE s 239 
 TRP   0.002   0.001   TRP r 136 
 HIS   0.007   0.002   HIS s 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.21 ( 6970)
  covalent geometry    : angle       0.95038 /  0.42 ( 9840)
  hydrogen bonds       : bond        0.07224 /  4.52 (  253)
  hydrogen bonds       : angle       5.90327 /  4.03 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: s  302 CYS cc_start: 0.2848 (OUTLIER) cc_final: 0.1687 (t)
REVERT: r   30 MET cc_start: 0.6204 (ptt) cc_final: 0.5954 (ptm)
REVERT: r   89 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.5755 (mmt180)
REVERT: r  220 THR cc_start: 0.4215 (OUTLIER) cc_final: 0.3932 (m)
  outliers start: 21
  outliers final: 13
  residues processed: 66
  average time/residue: 0.0699
  time to fit residues: 6.4495
Evaluate side-chains
  58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  302 CYS
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  229 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 187 GLN ** 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 = 0.4335 r_free = 0.4335 target = 0.116545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.109025 restraints weight = 41198.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.109469 restraints weight = 38748.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.110587 restraints weight = 28868.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.110444 restraints weight = 23418.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.110722 restraints weight = 19155.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4227 r_free = 0.4227    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4226 r_free = 0.4226    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (11 function evaluations)
r_final: 0.4226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.6048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6970  Z= 0.151
  Angle     :  0.859  10.949   9840  Z= 0.379
  Chirality :  0.062   0.616   1235
  Planarity :  0.004   0.063   1011
  Dihedral  : 17.360 177.386   1742
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.81 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 33.87 %
    Favored  : 61.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.29), residues: 755
  helix:  0.19 (0.34), residues: 224
  sheet: -1.98 (0.48), residues: 102
  loop : -1.92 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG s 296 
 TYR   0.011   0.001   TYR r  82 
 PHE   0.014   0.002   PHE s 239 
 TRP   0.005   0.001   TRP r 136 
 HIS   0.002   0.001   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 6970)
  covalent geometry    : angle       0.85855 /  0.38 ( 9840)
  hydrogen bonds       : bond        0.06725 /  4.30 (  253)
  hydrogen bonds       : angle       5.50705 /  3.77 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: s  226 CYS cc_start: 0.6140 (p) cc_final: 0.5521 (t)
REVERT: s  298 TYR cc_start: 0.6117 (m-80) cc_final: 0.5754 (m-80)
REVERT: r   89 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.5683 (mmt180)
REVERT: r  179 ASN cc_start: 0.6592 (p0) cc_final: 0.5968 (p0)
  outliers start: 17
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0741
  time to fit residues: 6.5976
Evaluate side-chains
  57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 50 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0010
   overall best weight:    1.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
s 301 GLN
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.116092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.108180 restraints weight = 40873.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.108224 restraints weight = 44419.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.109829 restraints weight = 32569.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.109586 restraints weight = 23494.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.109986 restraints weight = 20098.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4213 r_free = 0.4213    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4213 r_free = 0.4213    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.4213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5838
moved from start:          0.6167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6970  Z= 0.157
  Angle     :  0.850  11.140   9840  Z= 0.377
  Chirality :  0.061   0.600   1235
  Planarity :  0.004   0.065   1011
  Dihedral  : 17.301 176.622   1742
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.68 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 34.13 %
    Favored  : 62.13 %
  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 are not related in a simple way.
  whole: -1.84 (0.29), residues: 755
  helix:  0.18 (0.34), residues: 224
  sheet: -1.91 (0.48), residues: 102
  loop : -1.86 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG s 285 
 TYR   0.011   0.002   TYR s 278 
 PHE   0.016   0.002   PHE s 239 
 TRP   0.003   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.16 ( 6970)
  covalent geometry    : angle       0.84974 /  0.38 ( 9840)
  hydrogen bonds       : bond        0.06582 /  4.12 (  253)
  hydrogen bonds       : angle       5.50649 /  3.77 (  680)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: s  226 CYS cc_start: 0.6116 (p) cc_final: 0.5550 (t)
REVERT: r   89 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.5682 (mmt180)
  outliers start: 14
  outliers final: 12
  residues processed: 56
  average time/residue: 0.0715
  time to fit residues: 5.5623
Evaluate side-chains
  57 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  297 LEU
Chi-restraints excluded: chain s residue  306 HIS
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   70 CYS
Chi-restraints excluded: chain r residue   72 VAL
Chi-restraints excluded: chain r residue   73 VAL
Chi-restraints excluded: chain r residue   74 ILE
Chi-restraints excluded: chain r residue   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:   20.0000
   chunk 81 optimal weight:    3.9990
   chunk 71 optimal weight:   50.0000
   chunk 68 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 187 GLN ** 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 = 0.4309 r_free = 0.4309 target = 0.115280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.108309 restraints weight = 41331.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.108507 restraints weight = 38791.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.108982 restraints weight = 32695.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.108930 restraints weight = 28229.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.109235 restraints weight = 27461.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4192 r_free = 0.4192    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4192 r_free = 0.4192    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5816
moved from start:          0.6349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6970  Z= 0.175
  Angle     :  0.880  11.986   9840  Z= 0.389
  Chirality :  0.062   0.599   1235
  Planarity :  0.005   0.063   1011
  Dihedral  : 17.381 175.054   1742
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.40 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 33.87 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.29), residues: 755
  helix:  0.03 (0.33), residues: 225
  sheet: -1.94 (0.48), residues: 102
  loop : -1.85 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG s 273 
 TYR   0.011   0.002   TYR s 278 
 PHE   0.015   0.002   PHE s 239 
 TRP   0.004   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 306 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.17 ( 6970)
  covalent geometry    : angle       0.87996 /  0.39 ( 9840)
  hydrogen bonds       : bond        0.06628 /  4.17 (  253)
  hydrogen bonds       : angle       5.62085 /  3.85 (  680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1272.09 seconds
wall clock time: 22 minutes 36.42 seconds (1356.42 seconds total)