Starting phenix.real_space_refine
on Wed Feb 12 01:57:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_10774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_10774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_10774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_10774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ybv_10774/02_2025/6ybv_10774.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 12, 'rna3p': 62}
    Chain: "k"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Classifications: {'RNA': 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: 36
          Planarities with less than four sites: {'  A%rna2p_pur:plan': 1, '  A%rna2p_pur:plan2': 1, '  A%rna3p_pur:plan2': 2, '  A%rna3p_pur:plan': 2}
          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: {'GLN:plan1': 13, 'ASP:plan': 9, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 17}
          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: 7.29, per 1000 atoms: 1.08
  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: 1.91
  Conformation dependent library (CDL) restraints added in 788.5 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: 2.25
  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: 2.14

  Time building geometry restraints manager: 2.20 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=" C5'   G w  10 "
       pdb=" C4'   G w  10 "
    ideal  model  delta    sigma   weight residual
    1.508  1.480  0.028 1.50e-02 4.44e+03 3.59e+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
  ... (remaining 6965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 9310
        3.00 -     6.01: 484
        6.01 -     9.01: 35
        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=" C4'   G w  52 "
        pdb=" C3'   G w  52 "
        pdb=" O3'   G w  52 "
      ideal   model   delta    sigma   weight residual
     113.00  120.35   -7.35 1.50e+00 4.44e-01 2.40e+01
  ... (remaining 9835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.56: 3765
       24.56 -    49.11: 386
       49.11 -    73.67: 141
       73.67 -    98.23: 18
       98.23 -   122.78: 2
  Dihedral angle restraints: 4312
    sinusoidal: 2090
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" O4'   C w  73 "
           pdb=" C1'   C w  73 "
           pdb=" N1    C w  73 "
           pdb=" C2    C w  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -44.83  -83.17     1      1.70e+01 3.46e-03 2.93e+01
  dihedral pdb=" O4'   A k  17 "
           pdb=" C2'   A k  17 "
           pdb=" C1'   A k  17 "
           pdb=" C3'   A k  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.51   34.51     1      8.00e+00 1.56e-02 2.64e+01
  dihedral pdb=" O4'   A k  16 "
           pdb=" C2'   A k  16 "
           pdb=" C1'   A k  16 "
           pdb=" C3'   A k  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.08   34.08     1      8.00e+00 1.56e-02 2.58e+01
  ... (remaining 4309 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 883
       0.068 -    0.136: 271
       0.136 -    0.204: 68
       0.204 -    0.272: 9
       0.272 -    0.340: 4
  Chirality restraints: 1235
  Sorted by residual:
  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      2.45    2.11    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  VAL r  34 "
            pdb=" CA  VAL r  34 "
            pdb=" CG1 VAL r  34 "
            pdb=" CG2 VAL r  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO t 168 "
            pdb=" N   PRO t 168 "
            pdb=" C   PRO t 168 "
            pdb=" CB  PRO t 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.34e+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:             7.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5583
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      :  0.008   0.126   6970  Z= 0.532
  Angle     :  1.466  15.017   9840  Z= 0.842
  Chirality :  0.071   0.340   1235
  Planarity :  0.009   0.069   1011
  Dihedral  : 21.435 122.782   2868
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.009   0.004   TRP r 136 
 HIS   0.007   0.003   HIS r 155 
 PHE   0.032   0.005   PHE r 131 
 TYR   0.030   0.004   TYR s 176 
 ARG   0.016   0.002   ARG s 285 

*********************** 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  : 0.628 
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: 0.3052 (mtt) cc_final: 0.0831 (ttt)
  outliers start: 25
  outliers final: 6
  residues processed: 120
  average time/residue: 0.2710
  time to fit residues: 39.8802
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  : 0.639 
-------------------------------------------------------------------------------
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 69 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 41 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
s 181 ASN
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 = 0.4351 r_free = 0.4351 target = 0.117131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.110446 restraints weight = 41920.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.110488 restraints weight = 45841.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.111120 restraints weight = 34306.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4239 r_free = 0.4239    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4234 r_free = 0.4234    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.4234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5713
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   6970  Z= 0.255
  Angle     :  0.745   8.196   9840  Z= 0.401
  Chirality :  0.046   0.220   1235
  Planarity :  0.005   0.059   1011
  Dihedral  : 21.086 109.667   2021
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.03 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 29.60 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.27), residues: 755
  helix: -0.22 (0.32), residues: 217
  sheet: -0.28 (0.45), residues: 116
  loop : -2.07 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP r 136 
 HIS   0.016   0.003   HIS s 306 
 PHE   0.012   0.002   PHE r  13 
 TYR   0.021   0.002   TYR r 150 
 ARG   0.004   0.001   ARG r 234 

*********************** 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
  73 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: s  204 MET cc_start: 0.3889 (pmm) cc_final: 0.2769 (pmm)
REVERT: r   89 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.5072 (mmt180)
REVERT: r  121 TYR cc_start: 0.2927 (OUTLIER) cc_final: 0.1500 (m-80)
REVERT: r  182 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6768 (ttp80)
  outliers start: 18
  outliers final: 6
  residues processed: 73
  average time/residue: 0.2372
  time to fit residues: 22.2607
Evaluate side-chains
  50 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  280 THR
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  278 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 132 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.114063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.106721 restraints weight = 41555.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.107143 restraints weight = 39490.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.107538 restraints weight = 32553.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4177 r_free = 0.4177    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4177 r_free = 0.4177    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5910
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   6970  Z= 0.334
  Angle     :  0.831  12.130   9840  Z= 0.433
  Chirality :  0.048   0.206   1235
  Planarity :  0.006   0.065   1011
  Dihedral  : 21.172 127.587   2018
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.68 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 30.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.27), residues: 755
  helix: -0.42 (0.31), residues: 219
  sheet: -0.64 (0.46), residues: 117
  loop : -2.30 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP r 136 
 HIS   0.004   0.001   HIS s 235 
 PHE   0.030   0.003   PHE s 239 
 TYR   0.022   0.002   TYR r  82 
 ARG   0.005   0.001   ARG s 296 

*********************** 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
  74 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.675 
Fit side-chains
REVERT: r   89 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.5555 (mmt180)
REVERT: r  141 LYS cc_start: 0.7518 (mmmt) cc_final: 0.7275 (tppt)
REVERT: r  182 ARG cc_start: 0.7194 (mtm180) cc_final: 0.6778 (ttp80)
  outliers start: 24
  outliers final: 10
  residues processed: 73
  average time/residue: 0.2086
  time to fit residues: 20.1478
Evaluate side-chains
  53 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain r residue   20 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  121 TYR
Chi-restraints excluded: chain r residue  242 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 1 optimal weight:    0.2980
   chunk 7 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** s 221 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 = 0.4351 r_free = 0.4351 target = 0.117291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.108889 restraints weight = 40603.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.109937 restraints weight = 28089.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.110620 restraints weight = 21095.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4221 r_free = 0.4221    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4221 r_free = 0.4221    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5826
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6970  Z= 0.163
  Angle     :  0.632   8.439   9840  Z= 0.333
  Chirality :  0.044   0.189   1235
  Planarity :  0.004   0.047   1011
  Dihedral  : 20.782 123.130   2016
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.37 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 29.60 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.28), residues: 755
  helix:  0.08 (0.32), residues: 225
  sheet: -0.35 (0.52), residues: 85
  loop : -1.98 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 230 
 PHE   0.018   0.002   PHE s 239 
 TYR   0.017   0.002   TYR r 150 
 ARG   0.005   0.001   ARG s 211 

*********************** 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
  75 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.677 
Fit side-chains
REVERT: s  204 MET cc_start: 0.3816 (pmm) cc_final: 0.3088 (pmm)
REVERT: s  226 CYS cc_start: 0.5631 (t) cc_final: 0.4858 (t)
REVERT: r   89 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.5350 (mmt180)
REVERT: r  121 TYR cc_start: 0.3231 (OUTLIER) cc_final: 0.1755 (m-80)
REVERT: r  182 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6803 (ttp80)
REVERT: r  220 THR cc_start: 0.4739 (OUTLIER) cc_final: 0.4494 (m)
  outliers start: 21
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1965
  time to fit residues: 18.8652
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  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
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  121 TYR
Chi-restraints excluded: chain r residue  189 VAL
Chi-restraints excluded: chain r residue  220 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** s 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r  40 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 = 0.4259 r_free = 0.4259 target = 0.111834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.105340 restraints weight = 40669.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.105118 restraints weight = 41380.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.105972 restraints weight = 31612.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4148 r_free = 0.4148    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4148 r_free = 0.4148    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6025
moved from start:          0.4923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088   6970  Z= 0.448
  Angle     :  0.978  18.229   9840  Z= 0.499
  Chirality :  0.052   0.208   1235
  Planarity :  0.007   0.061   1011
  Dihedral  : 21.500 127.596   2016
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 22.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 10.20 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 31.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.26), residues: 755
  helix: -0.96 (0.29), residues: 223
  sheet: -2.44 (0.49), residues: 86
  loop : -2.45 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP r 136 
 HIS   0.009   0.002   HIS s 306 
 PHE   0.019   0.003   PHE s 299 
 TYR   0.028   0.004   TYR r 150 
 ARG   0.007   0.001   ARG s 296 

*********************** 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
  65 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.597 
Fit side-chains
REVERT: s  226 CYS cc_start: 0.5451 (t) cc_final: 0.5065 (t)
REVERT: r   89 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.5663 (mmt180)
REVERT: r  220 THR cc_start: 0.3052 (OUTLIER) cc_final: 0.2847 (m)
  outliers start: 21
  outliers final: 10
  residues processed: 63
  average time/residue: 0.1897
  time to fit residues: 16.2548
Evaluate side-chains
  54 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  258 ILE
Chi-restraints excluded: chain s residue  279 VAL
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   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  229 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 71 optimal weight:   40.0000
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
s 221 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.115583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.108392 restraints weight = 41426.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.108335 restraints weight = 40452.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.109344 restraints weight = 32906.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4217 r_free = 0.4217    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4217 r_free = 0.4217    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.4877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6970  Z= 0.173
  Angle     :  0.659   9.230   9840  Z= 0.342
  Chirality :  0.044   0.186   1235
  Planarity :  0.004   0.044   1011
  Dihedral  : 20.948 120.094   2016
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.83 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 33.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.28), residues: 755
  helix:  0.00 (0.32), residues: 225
  sheet: -1.34 (0.52), residues: 84
  loop : -2.13 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP r 136 
 HIS   0.002   0.001   HIS s 230 
 PHE   0.010   0.001   PHE s 239 
 TYR   0.016   0.002   TYR r  82 
 ARG   0.005   0.000   ARG s 296 

*********************** 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
  70 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.677 
Fit side-chains
REVERT: s  204 MET cc_start: 0.4075 (pmm) cc_final: 0.2893 (pmm)
REVERT: r   89 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.5484 (mmt180)
REVERT: r  182 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6666 (ttp80)
REVERT: r  220 THR cc_start: 0.4403 (OUTLIER) cc_final: 0.4103 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 70
  average time/residue: 0.2404
  time to fit residues: 23.1079
Evaluate side-chains
  58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
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  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  242 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0970
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:   20.0000
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.115071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.107606 restraints weight = 40858.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.107775 restraints weight = 41271.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.108802 restraints weight = 31637.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5873
moved from start:          0.5071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6970  Z= 0.206
  Angle     :  0.678  12.183   9840  Z= 0.350
  Chirality :  0.044   0.196   1235
  Planarity :  0.005   0.059   1011
  Dihedral  : 20.930 109.902   2016
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.14 %
    Favored  : 90.60 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.29), residues: 755
  helix:  0.04 (0.33), residues: 223
  sheet: -1.41 (0.54), residues: 75
  loop : -2.06 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP r 136 
 HIS   0.004   0.001   HIS s 235 
 PHE   0.024   0.002   PHE s 239 
 TYR   0.020   0.002   TYR s 274 
 ARG   0.003   0.000   ARG s 211 

*********************** 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
  66 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.648 
Fit side-chains
REVERT: s  188 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.4311 (ptt-90)
REVERT: r   89 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5524 (mmt180)
REVERT: r  121 TYR cc_start: 0.3441 (OUTLIER) cc_final: 0.2085 (m-80)
REVERT: r  182 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6554 (ttp80)
REVERT: r  220 THR cc_start: 0.4463 (OUTLIER) cc_final: 0.4165 (m)
REVERT: r  255 MET cc_start: 0.5235 (mmm) cc_final: 0.4868 (mpp)
  outliers start: 20
  outliers final: 12
  residues processed: 64
  average time/residue: 0.2037
  time to fit residues: 17.4655
Evaluate side-chains
  60 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  188 ARG
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  258 ILE
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
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  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  242 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 50 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 66 optimal weight:   30.0000
   chunk 13 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    2.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.114238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.107019 restraints weight = 41165.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.107242 restraints weight = 46418.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.107809 restraints weight = 33739.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4184 r_free = 0.4184    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4184 r_free = 0.4184    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5907
moved from start:          0.5435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6970  Z= 0.251
  Angle     :  0.725  12.055   9840  Z= 0.373
  Chirality :  0.045   0.200   1235
  Planarity :  0.005   0.062   1011
  Dihedral  : 21.055 102.837   2016
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.93 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 30.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.28), residues: 755
  helix: -0.17 (0.32), residues: 223
  sheet: -1.90 (0.52), residues: 84
  loop : -2.13 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP r 136 
 HIS   0.005   0.002   HIS s 235 
 PHE   0.019   0.002   PHE s 239 
 TYR   0.019   0.002   TYR r 150 
 ARG   0.004   0.001   ARG s 211 

*********************** 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
  66 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 0.621 
Fit side-chains
REVERT: s  188 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.5141 (ptt-90)
REVERT: s  215 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7777 (mmtm)
REVERT: r   89 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.5743 (mmt180)
REVERT: r  182 ARG cc_start: 0.6989 (mtm180) cc_final: 0.6537 (ttp80)
REVERT: r  220 THR cc_start: 0.3944 (OUTLIER) cc_final: 0.3667 (m)
  outliers start: 23
  outliers final: 15
  residues processed: 63
  average time/residue: 0.2083
  time to fit residues: 17.4552
Evaluate side-chains
  62 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  188 ARG
Chi-restraints excluded: chain s residue  215 LYS
Chi-restraints excluded: chain s residue  217 THR
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  250 ILE
Chi-restraints excluded: chain s residue  258 ILE
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   22 VAL
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  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Chi-restraints excluded: chain r residue  242 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 69 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
s 301 GLN
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 179 ASN ** 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 = 0.4355 r_free = 0.4355 target = 0.117079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.109012 restraints weight = 41618.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.109900 restraints weight = 29947.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.110505 restraints weight = 23091.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4225 r_free = 0.4225    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4225 r_free = 0.4225    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5777
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6970  Z= 0.151
  Angle     :  0.608   9.379   9840  Z= 0.312
  Chirality :  0.042   0.252   1235
  Planarity :  0.004   0.064   1011
  Dihedral  : 20.503 104.750   2016
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.75 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 32.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.29), residues: 755
  helix:  0.58 (0.34), residues: 226
  sheet: -1.96 (0.43), residues: 118
  loop : -1.98 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP r 136 
 HIS   0.003   0.001   HIS s 235 
 PHE   0.014   0.001   PHE s 239 
 TYR   0.014   0.001   TYR r  82 
 ARG   0.002   0.000   ARG r  55 

*********************** 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
  70 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.533 
Fit side-chains
REVERT: s  188 ARG cc_start: 0.4842 (OUTLIER) cc_final: 0.4569 (ptt-90)
REVERT: r   89 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.5462 (mmt180)
REVERT: r  121 TYR cc_start: 0.3253 (OUTLIER) cc_final: 0.2035 (m-80)
REVERT: r  220 THR cc_start: 0.4642 (OUTLIER) cc_final: 0.4321 (m)
  outliers start: 17
  outliers final: 6
  residues processed: 69
  average time/residue: 0.2047
  time to fit residues: 18.7715
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  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  188 ARG
Chi-restraints excluded: chain s residue  258 ILE
Chi-restraints excluded: chain r residue   48 LEU
Chi-restraints excluded: chain r residue   70 CYS
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  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 73 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
** s 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4271 r_free = 0.4271 target = 0.112784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.105800 restraints weight = 41373.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.106278 restraints weight = 37566.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.107009 restraints weight = 28134.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4167 r_free = 0.4167    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4167 r_free = 0.4167    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          0.5883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   6970  Z= 0.344
  Angle     :  0.841  15.725   9840  Z= 0.425
  Chirality :  0.048   0.262   1235
  Planarity :  0.006   0.063   1011
  Dihedral  : 21.053 104.570   2014
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 10.86 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 32.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.29), residues: 755
  helix: -0.27 (0.32), residues: 223
  sheet: -2.05 (0.48), residues: 93
  loop : -2.08 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP r 136 
 HIS   0.005   0.001   HIS s 306 
 PHE   0.023   0.002   PHE s 239 
 TYR   0.023   0.003   TYR r 150 
 ARG   0.004   0.001   ARG s 296 

********************** 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
  62 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: r   89 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.5836 (mmt180)
REVERT: r  121 TYR cc_start: 0.3546 (OUTLIER) cc_final: 0.2377 (m-80)
REVERT: r  220 THR cc_start: 0.3914 (OUTLIER) cc_final: 0.3577 (m)
  outliers start: 14
  outliers final: 6
  residues processed: 60
  average time/residue: 0.2321
  time to fit residues: 18.2196
Evaluate side-chains
  53 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   30 MET
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   89 ARG
Chi-restraints excluded: chain r residue  119 LEU
Chi-restraints excluded: chain r residue  121 TYR
Chi-restraints excluded: chain r residue  220 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** s 301 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 = 0.4245 r_free = 0.4245 target = 0.111213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.104359 restraints weight = 40757.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.104703 restraints weight = 38801.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.105322 restraints weight = 29760.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4135 r_free = 0.4135    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4135 r_free = 0.4135    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6050
moved from start:          0.6362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.111   6970  Z= 0.385
  Angle     :  0.933  16.724   9840  Z= 0.469
  Chirality :  0.051   0.249   1235
  Planarity :  0.006   0.065   1011
  Dihedral  : 21.397 102.082   2014
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 11.92 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 32.27 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.28), residues: 755
  helix: -0.89 (0.31), residues: 224
  sheet: -2.85 (0.47), residues: 95
  loop : -2.34 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP r 136 
 HIS   0.005   0.001   HIS s 306 
 PHE   0.020   0.002   PHE s 239 
 TYR   0.023   0.003   TYR r 150 
 ARG   0.005   0.001   ARG s 296 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2348.71 seconds
wall clock time: 43 minutes 5.38 seconds (2585.38 seconds total)