Starting phenix.real_space_refine
on Wed Mar 12 01:37:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ybv_10774/03_2025/6ybv_10774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ybv_10774/03_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_10774/03_2025/6ybv_10774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2025/6ybv_10774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_2025/6ybv_10774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ybv_10774/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.28, 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: 1.82
  Conformation dependent library (CDL) restraints added in 712.8 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: 2.37
  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: 2.34

  Time building geometry restraints manager: 2.14 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:             9.620
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.180
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.390
-------------------------------------------------------------------------------
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  : 0.599 
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: 0.2683
  time to fit residues: 39.3983
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  : 0.607 
-------------------------------------------------------------------------------
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 = 0.117132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.110507 restraints weight = 41920.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.110559 restraints weight = 44618.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.111118 restraints weight = 33867.445|
|-----------------------------------------------------------------------------|
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 = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5717
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 : 15.18
  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  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: s  204 MET cc_start: 0.3896 (pmm) cc_final: 0.2775 (pmm)
REVERT: r   89 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.5061 (mmt180)
REVERT: r  121 TYR cc_start: 0.2940 (OUTLIER) cc_final: 0.1512 (m-80)
REVERT: r  182 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6777 (ttp80)
  outliers start: 18
  outliers final: 6
  residues processed: 73
  average time/residue: 0.2351
  time to fit residues: 21.8311
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  : 0.647 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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 = 0.4317 r_free = 0.4317 target = 0.115121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.107419 restraints weight = 41633.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.107759 restraints weight = 39204.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.108405 restraints weight = 30079.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4192 r_free = 0.4192    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4192 r_free = 0.4192    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5868
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6970  Z= 0.273
  Angle     :  0.750  11.563   9840  Z= 0.394
  Chirality :  0.046   0.205   1235
  Planarity :  0.005   0.060   1011
  Dihedral  : 21.021 120.660   2018
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.36 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 30.13 %
    Favored  : 64.27 %
  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: -1.94 (0.28), residues: 755
  helix: -0.20 (0.32), residues: 220
  sheet: -0.81 (0.44), residues: 128
  loop : -2.14 (0.27), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP r 136 
 HIS   0.007   0.002   HIS s 306 
 PHE   0.027   0.002   PHE s 239 
 TYR   0.015   0.002   TYR r 109 
 ARG   0.004   0.001   ARG s 231 

*********************** 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
  71 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 50
  time to evaluate  : 0.618 
Fit side-chains
REVERT: r   89 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.5452 (mmt180)
REVERT: r  182 ARG cc_start: 0.7316 (mtm180) cc_final: 0.6803 (ttp80)
  outliers start: 21
  outliers final: 10
  residues processed: 70
  average time/residue: 0.2067
  time to fit residues: 19.3683
Evaluate side-chains
  54 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   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  189 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0060
   chunk 7 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0040
   overall best weight:    1.1612

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.117617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.109467 restraints weight = 41125.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.110492 restraints weight = 27842.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.111116 restraints weight = 20772.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4224 r_free = 0.4224    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4224 r_free = 0.4224    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5820
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6970  Z= 0.168
  Angle     :  0.618   8.851   9840  Z= 0.328
  Chirality :  0.043   0.191   1235
  Planarity :  0.004   0.046   1011
  Dihedral  : 20.725 122.314   2016
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.77 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 28.00 %
    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: -1.56 (0.28), residues: 755
  helix:  0.20 (0.32), residues: 225
  sheet: -0.69 (0.46), residues: 110
  loop : -1.89 (0.28), residues: 420

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   0.015   0.001   PHE s 239 
 TYR   0.015   0.001   TYR r  82 
 ARG   0.004   0.000   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
  79 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.492 
Fit side-chains
REVERT: s  226 CYS cc_start: 0.5604 (t) cc_final: 0.4877 (t)
REVERT: r   89 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.5419 (mmt180)
REVERT: r  121 TYR cc_start: 0.3257 (OUTLIER) cc_final: 0.1892 (m-80)
REVERT: r  182 ARG cc_start: 0.7492 (mtm180) cc_final: 0.6784 (ttp80)
REVERT: r  220 THR cc_start: 0.4816 (OUTLIER) cc_final: 0.4587 (m)
  outliers start: 24
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1830
  time to fit residues: 19.0150
Evaluate side-chains
  61 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain r residue  242 LEU
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:   30.0000
   chunk 10 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0020
   chunk 81 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 47 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.7994

-------------------------------------------------------------------------------
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  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.115003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.106958 restraints weight = 40870.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.107961 restraints weight = 27770.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.108637 restraints weight = 20536.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4191 r_free = 0.4191    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 = 0.4191 r_free = 0.4191    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5931
moved from start:          0.4400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6970  Z= 0.279
  Angle     :  0.749  12.743   9840  Z= 0.388
  Chirality :  0.046   0.219   1235
  Planarity :  0.005   0.049   1011
  Dihedral  : 20.974 129.092   2016
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.08 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 31.20 %
    Favored  : 63.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.88 (0.28), residues: 755
  helix: -0.16 (0.31), residues: 224
  sheet: -0.79 (0.50), residues: 95
  loop : -2.03 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP r 136 
 HIS   0.004   0.001   HIS s 306 
 PHE   0.018   0.002   PHE s 299 
 TYR   0.016   0.002   TYR r 150 
 ARG   0.006   0.001   ARG s 211 

*********************** 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
  66 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.589 
Fit side-chains
REVERT: s  226 CYS cc_start: 0.5208 (t) cc_final: 0.4838 (t)
REVERT: r   89 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.5424 (mmt180)
REVERT: r  182 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6670 (ttp80)
REVERT: r  220 THR cc_start: 0.4469 (OUTLIER) cc_final: 0.4223 (m)
  outliers start: 21
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1941
  time to fit residues: 16.8933
Evaluate side-chains
  58 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   45 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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 32 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4339 r_free = 0.4339 target = 0.116315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.109776 restraints weight = 41616.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.109905 restraints weight = 35998.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.110586 restraints weight = 28430.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4234
|-occupancy refinement: start-------------------------------------------------|
| 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:        3 |
|-----------------------------------------------------------------------------|
|-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:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5741
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6970  Z= 0.163
  Angle     :  0.616   8.248   9840  Z= 0.323
  Chirality :  0.043   0.211   1235
  Planarity :  0.004   0.045   1011
  Dihedral  : 20.689 124.204   2016
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.43 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 32.53 %
    Favored  : 62.40 %
  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: -1.47 (0.29), residues: 755
  helix:  0.44 (0.33), residues: 225
  sheet: -0.67 (0.51), residues: 94
  loop : -1.91 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP r 136 
 HIS   0.002   0.001   HIS s 230 
 PHE   0.010   0.001   PHE s 299 
 TYR   0.013   0.002   TYR r  82 
 ARG   0.003   0.000   ARG r 113 

*********************** 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
  66 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 47
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: s  295 THR cc_start: 0.4102 (OUTLIER) cc_final: 0.3894 (t)
REVERT: r   89 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.5338 (mmt180)
REVERT: r  121 TYR cc_start: 0.3096 (OUTLIER) cc_final: 0.1743 (m-80)
REVERT: r  182 ARG cc_start: 0.7503 (mtm180) cc_final: 0.6744 (ttp80)
REVERT: r  220 THR cc_start: 0.4429 (OUTLIER) cc_final: 0.4102 (m)
  outliers start: 19
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1843
  time to fit residues: 16.4482
Evaluate side-chains
  59 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain s residue  295 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:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 5 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.115759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.108907 restraints weight = 40931.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.109088 restraints weight = 37808.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.109448 restraints weight = 29971.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4211 r_free = 0.4211    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4211 r_free = 0.4211    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5780
moved from start:          0.4807

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= 0.184
  Angle     :  0.630  10.501   9840  Z= 0.328
  Chirality :  0.043   0.169   1235
  Planarity :  0.004   0.040   1011
  Dihedral  : 20.718 121.015   2016
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.95 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 31.20 %
    Favored  : 62.40 %
  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: -1.52 (0.29), residues: 755
  helix:  0.36 (0.33), residues: 223
  sheet: -0.90 (0.55), residues: 74
  loop : -1.82 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 235 
 PHE   0.011   0.002   PHE s 222 
 TYR   0.017   0.002   TYR s 274 
 ARG   0.003   0.000   ARG r 113 

*********************** 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
  69 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.587 
Fit side-chains
REVERT: r   89 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5281 (mmt180)
REVERT: r  121 TYR cc_start: 0.3234 (OUTLIER) cc_final: 0.1840 (m-80)
REVERT: r  182 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6720 (ttp80)
REVERT: r  220 THR cc_start: 0.4458 (OUTLIER) cc_final: 0.4127 (m)
REVERT: r  272 GLN cc_start: 0.3946 (tp40) cc_final: 0.3217 (mp10)
  outliers start: 24
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1873
  time to fit residues: 16.9415
Evaluate side-chains
  59 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  224 ASP
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain r residue   20 VAL
Chi-restraints excluded: chain r residue   45 MET
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:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 66 optimal weight:   30.0000
   chunk 13 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.114052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.106353 restraints weight = 41067.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.106427 restraints weight = 42337.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.107695 restraints weight = 31430.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4182 r_free = 0.4182    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4182 r_free = 0.4182    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5962
moved from start:          0.5176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6970  Z= 0.282
  Angle     :  0.764  13.095   9840  Z= 0.393
  Chirality :  0.047   0.270   1235
  Planarity :  0.005   0.048   1011
  Dihedral  : 21.032 106.577   2016
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.87 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 32.80 %
    Favored  : 61.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.99 (0.28), residues: 755
  helix: -0.17 (0.32), residues: 223
  sheet: -1.64 (0.52), residues: 84
  loop : -1.93 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP r 136 
 HIS   0.004   0.001   HIS s 306 
 PHE   0.014   0.002   PHE s 299 
 TYR   0.021   0.002   TYR r 150 
 ARG   0.006   0.001   ARG s 296 

*********************** 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
  63 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.651 
Fit side-chains
REVERT: r   89 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.5347 (mmt180)
REVERT: r  182 ARG cc_start: 0.7349 (mtm180) cc_final: 0.6656 (ttp80)
REVERT: r  220 THR cc_start: 0.4506 (OUTLIER) cc_final: 0.4186 (m)
  outliers start: 20
  outliers final: 12
  residues processed: 62
  average time/residue: 0.1842
  time to fit residues: 15.6581
Evaluate side-chains
  55 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  221 ASN
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  279 VAL
Chi-restraints excluded: chain s residue  280 THR
Chi-restraints excluded: chain 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  242 LEU
Chi-restraints excluded: chain r residue  268 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 69 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0870
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
s 221 ASN
** r 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.116065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.108167 restraints weight = 41525.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.108578 restraints weight = 39276.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.109775 restraints weight = 30102.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4221 r_free = 0.4221    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4221 r_free = 0.4221    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5829
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6970  Z= 0.166
  Angle     :  0.640  10.132   9840  Z= 0.329
  Chirality :  0.043   0.190   1235
  Planarity :  0.004   0.039   1011
  Dihedral  : 20.629 102.218   2016
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.42 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 34.67 %
    Favored  : 61.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.32 (0.34), residues: 225
  sheet: -1.85 (0.45), residues: 115
  loop : -1.84 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP r 136 
 HIS   0.003   0.001   HIS s 235 
 PHE   0.008   0.001   PHE s 239 
 TYR   0.013   0.001   TYR r  82 
 ARG   0.005   0.000   ARG s 296 

*********************** 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
  60 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: r   89 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.5382 (mmt180)
REVERT: r  121 TYR cc_start: 0.3447 (OUTLIER) cc_final: 0.2200 (m-80)
REVERT: r  220 THR cc_start: 0.4329 (OUTLIER) cc_final: 0.4041 (m)
REVERT: r  255 MET cc_start: 0.5186 (mmm) cc_final: 0.4939 (mpp)
  outliers start: 14
  outliers final: 9
  residues processed: 60
  average time/residue: 0.1828
  time to fit residues: 15.0938
Evaluate side-chains
  52 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  280 THR
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 48 optimal weight:    0.2980
   chunk 73 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
** r 132 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 = 0.4302 r_free = 0.4302 target = 0.114477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.107616 restraints weight = 41969.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.107812 restraints weight = 39986.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.108955 restraints weight = 30966.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4203 r_free = 0.4203    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4203 r_free = 0.4203    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5863
moved from start:          0.5503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6970  Z= 0.252
  Angle     :  0.728  13.160   9840  Z= 0.371
  Chirality :  0.045   0.256   1235
  Planarity :  0.005   0.062   1011
  Dihedral  : 20.830 100.454   2015
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.14 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 34.93 %
    Favored  : 61.33 %
  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: -1.88 (0.29), residues: 755
  helix:  0.04 (0.33), residues: 223
  sheet: -1.84 (0.48), residues: 103
  loop : -1.85 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP r 136 
 HIS   0.004   0.001   HIS s 306 
 PHE   0.014   0.002   PHE s 299 
 TYR   0.018   0.002   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
  54 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
REVERT: r   89 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.5485 (mmt180)
REVERT: r  121 TYR cc_start: 0.3550 (OUTLIER) cc_final: 0.2360 (m-80)
REVERT: r  220 THR cc_start: 0.4204 (OUTLIER) cc_final: 0.3854 (m)
REVERT: r  255 MET cc_start: 0.5234 (mmm) cc_final: 0.4851 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 54
  average time/residue: 0.2054
  time to fit residues: 15.1692
Evaluate side-chains
  52 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain s residue  244 LEU
Chi-restraints excluded: chain s residue  280 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0070
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    3.0006

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.113372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.106382 restraints weight = 41183.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.106752 restraints weight = 38391.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.107141 restraints weight = 31723.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4162 r_free = 0.4162    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4162 r_free = 0.4162    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5972
moved from start:          0.5948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   6970  Z= 0.293
  Angle     :  0.804  13.949   9840  Z= 0.409
  Chirality :  0.047   0.232   1235
  Planarity :  0.005   0.065   1011
  Dihedral  : 21.014 100.262   2015
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 11.26 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 33.07 %
    Favored  : 62.40 %
  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: -0.34 (0.32), residues: 223
  sheet: -2.21 (0.48), residues: 95
  loop : -1.99 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP r 136 
 HIS   0.004   0.001   HIS s 306 
 PHE   0.015   0.002   PHE s 299 
 TYR   0.024   0.002   TYR r 150 
 ARG   0.008   0.001   ARG s 200 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.31 seconds
wall clock time: 42 minutes 55.94 seconds (2575.94 seconds total)