Starting phenix.real_space_refine
on Fri Jun 13 20:25:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.cif"
  }
  resolution = 2.27
  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=   0.001 sd=   0.115
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     S      85      5.16       5
     Cl      1      4.86       5
     C   10130      2.51       5
     N    2555      2.21       5
     O    2710      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15486
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "D"
      Number of atoms: 3096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
      Conformer: "B"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
          bond proxies already assigned to first conformer: 3163
    Chain: "E"
      Number of atoms: 3096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
      Conformer: "B"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
          bond proxies already assigned to first conformer: 3163
    Chain: "C"
      Number of atoms: 3096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
      Conformer: "B"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
          bond proxies already assigned to first conformer: 3163
    Chain: "A"
      Number of atoms: 3096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
      Conformer: "B"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
          bond proxies already assigned to first conformer: 3163
    Chain: "B"
      Number of atoms: 3096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
      Conformer: "B"
        Number of residues, atoms: 376, 3089
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 11, 'TRANS': 364}
          bond proxies already assigned to first conformer: 3163
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' CL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 17.78, per 1000 atoms: 1.15
  Number of scatterers: 15486
  At special positions: 0
  Unit cell: (105.41, 106.24, 109.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      5     19.99
     Cl      1     17.00
     S      85     16.00
     O    2710      8.00
     N    2555      7.00
     C   10130      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: 3.99
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3590

  Finding SS restraints...
    Secondary structure from input PDB file:
      86 helices and 0 sheets defined
      70.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'D' and resid 6 through 10
    Processing helix  chain 'D' and resid 19 through 23
    Processing helix  chain 'D' and resid 27 through 53
      removed outlier: 5.757A  pdb=" N   ARG D  34 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   GLU D  35 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 71
      removed outlier: 3.782A  pdb=" N   GLN D  71 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 99
    Processing helix  chain 'D' and resid 103 through 114
    Processing helix  chain 'D' and resid 118 through 144
    Processing helix  chain 'D' and resid 144 through 151
    Processing helix  chain 'D' and resid 153 through 160
    Processing helix  chain 'D' and resid 164 through 174
    Processing helix  chain 'D' and resid 182 through 198
    Processing helix  chain 'D' and resid 203 through 230
    Processing helix  chain 'D' and resid 233 through 255
    Processing helix  chain 'D' and resid 259 through 263
    Processing helix  chain 'D' and resid 274 through 295
      removed outlier: 3.880A  pdb=" N   ALA D 291 " --> pdb=" O   TRP D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 324
    Processing helix  chain 'D' and resid 351 through 355
    Processing helix  chain 'E' and resid 6 through 10
    Processing helix  chain 'E' and resid 19 through 23
    Processing helix  chain 'E' and resid 27 through 53
      removed outlier: 5.759A  pdb=" N   ARG E  34 " --> pdb=" O   LYS E  30 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   GLU E  35 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 71
      removed outlier: 3.754A  pdb=" N   GLN E  71 " --> pdb=" O   ILE E  67 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 99
      removed outlier: 4.509A  pdb=" N   VAL E  78 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 114
    Processing helix  chain 'E' and resid 118 through 144
    Processing helix  chain 'E' and resid 144 through 151
    Processing helix  chain 'E' and resid 153 through 160
    Processing helix  chain 'E' and resid 164 through 174
    Processing helix  chain 'E' and resid 182 through 198
    Processing helix  chain 'E' and resid 203 through 230
    Processing helix  chain 'E' and resid 233 through 255
    Processing helix  chain 'E' and resid 259 through 263
    Processing helix  chain 'E' and resid 274 through 295
      removed outlier: 3.876A  pdb=" N   ALA E 291 " --> pdb=" O   TRP E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 306 through 324
    Processing helix  chain 'E' and resid 351 through 355
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 19 through 23
    Processing helix  chain 'C' and resid 27 through 53
      removed outlier: 5.754A  pdb=" N   ARG C  34 " --> pdb=" O   LYS C  30 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   GLU C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 71
      removed outlier: 3.780A  pdb=" N   GLN C  71 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 99
      removed outlier: 4.525A  pdb=" N   VAL C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 114
    Processing helix  chain 'C' and resid 118 through 144
    Processing helix  chain 'C' and resid 144 through 151
    Processing helix  chain 'C' and resid 153 through 160
    Processing helix  chain 'C' and resid 164 through 174
    Processing helix  chain 'C' and resid 182 through 198
    Processing helix  chain 'C' and resid 203 through 230
    Processing helix  chain 'C' and resid 233 through 255
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 274 through 295
      removed outlier: 3.884A  pdb=" N   ALA C 291 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 324
    Processing helix  chain 'C' and resid 351 through 355
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 19 through 23
    Processing helix  chain 'A' and resid 27 through 53
      removed outlier: 5.768A  pdb=" N   ARG A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   GLU A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 71
      removed outlier: 3.752A  pdb=" N   GLN A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 99
      removed outlier: 4.547A  pdb=" N   VAL A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 114
    Processing helix  chain 'A' and resid 118 through 144
    Processing helix  chain 'A' and resid 144 through 151
    Processing helix  chain 'A' and resid 153 through 160
    Processing helix  chain 'A' and resid 164 through 174
    Processing helix  chain 'A' and resid 182 through 198
    Processing helix  chain 'A' and resid 203 through 230
    Processing helix  chain 'A' and resid 233 through 255
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 274 through 295
      removed outlier: 3.876A  pdb=" N   ALA A 291 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 324
    Processing helix  chain 'A' and resid 351 through 355
    Processing helix  chain 'A' and resid 371 through 375
      removed outlier: 3.682A  pdb=" N   GLN A 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 19 through 23
    Processing helix  chain 'B' and resid 27 through 53
      removed outlier: 5.759A  pdb=" N   ARG B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   GLU B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 71
      removed outlier: 3.795A  pdb=" N   GLN B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 99
    Processing helix  chain 'B' and resid 103 through 114
    Processing helix  chain 'B' and resid 118 through 144
    Processing helix  chain 'B' and resid 144 through 151
    Processing helix  chain 'B' and resid 153 through 160
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 182 through 198
    Processing helix  chain 'B' and resid 203 through 230
    Processing helix  chain 'B' and resid 233 through 255
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 274 through 295
      removed outlier: 3.861A  pdb=" N   ALA B 291 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 324
    Processing helix  chain 'B' and resid 351 through 355

    981 hydrogen bonds defined for protein.
    2815 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.51

  Time building geometry restraints manager: 4.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4851
        1.34 -     1.46: 3691
        1.46 -     1.58: 7233
        1.58 -     1.70: 0
        1.70 -     1.81: 130
  Bond restraints: 15905
  Sorted by residual:
  bond pdb=" N   ASP B 155 "
       pdb=" CA  ASP B 155 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.23e-02 6.61e+03 2.78e+00
  bond pdb=" C   ASP B 155 "
       pdb=" O   ASP B 155 "
    ideal  model  delta    sigma   weight residual
    1.237  1.224  0.013 1.19e-02 7.06e+03 1.14e+00
  bond pdb=" C   ILE B 154 "
       pdb=" N   ASP B 155 "
    ideal  model  delta    sigma   weight residual
    1.335  1.323  0.012 1.36e-02 5.41e+03 7.95e-01
  bond pdb=" CA  ARG A 356 "
       pdb=" CB  ARG A 356 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.50e-01
  bond pdb=" CA  ARG E 356 "
       pdb=" CB  ARG E 356 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.014 1.69e-02 3.50e+03 7.36e-01
  ... (remaining 15900 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 21099
        1.41 -     2.82: 402
        2.82 -     4.23: 80
        4.23 -     5.64: 17
        5.64 -     7.05: 7
  Bond angle restraints: 21605
  Sorted by residual:
  angle pdb=" C   LEU B 355 "
        pdb=" N   ARG B 356 "
        pdb=" CA  ARG B 356 "
      ideal   model   delta    sigma   weight residual
     121.54  128.59   -7.05 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" C   LEU A 355 "
        pdb=" N   ARG A 356 "
        pdb=" CA  ARG A 356 "
      ideal   model   delta    sigma   weight residual
     121.54  128.52   -6.98 1.91e+00 2.74e-01 1.34e+01
  angle pdb=" C   LEU C 355 "
        pdb=" N   ARG C 356 "
        pdb=" CA  ARG C 356 "
      ideal   model   delta    sigma   weight residual
     121.54  128.50   -6.96 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" C   LEU D 355 "
        pdb=" N   ARG D 356 "
        pdb=" CA  ARG D 356 "
      ideal   model   delta    sigma   weight residual
     121.54  128.48   -6.94 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" C   LEU E 355 "
        pdb=" N   ARG E 356 "
        pdb=" CA  ARG E 356 "
      ideal   model   delta    sigma   weight residual
     121.54  128.46   -6.92 1.91e+00 2.74e-01 1.31e+01
  ... (remaining 21600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 8459
       17.99 -    35.97: 614
       35.97 -    53.96: 157
       53.96 -    71.94: 40
       71.94 -    89.93: 10
  Dihedral angle restraints: 9280
    sinusoidal: 3685
      harmonic: 5595
  Sorted by residual:
  dihedral pdb=" CA  ASP B 268 "
           pdb=" CB  ASP B 268 "
           pdb=" CG  ASP B 268 "
           pdb=" OD1 ASP B 268 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.11   59.11     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  VAL A 114 "
           pdb=" C   VAL A 114 "
           pdb=" N   HIS A 115 "
           pdb=" CA  HIS A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.12  -16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  VAL D 114 "
           pdb=" C   VAL D 114 "
           pdb=" N   HIS D 115 "
           pdb=" CA  HIS D 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.33  -16.67     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 9277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1479
       0.029 -    0.058: 629
       0.058 -    0.087: 161
       0.087 -    0.116: 71
       0.116 -    0.144: 10
  Chirality restraints: 2350
  Sorted by residual:
  chirality pdb=" CA  VAL B 232 "
            pdb=" N   VAL B 232 "
            pdb=" C   VAL B 232 "
            pdb=" CB  VAL B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  VAL E 232 "
            pdb=" N   VAL E 232 "
            pdb=" C   VAL E 232 "
            pdb=" CB  VAL E 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  VAL A 232 "
            pdb=" N   VAL A 232 "
            pdb=" C   VAL A 232 "
            pdb=" CB  VAL A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.92e-01
  ... (remaining 2347 not shown)

  Planarity restraints: 2725
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 154 "   -0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   ILE B 154 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ILE B 154 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B 155 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  80 "   -0.012 2.00e-02 2.50e+03   1.01e-02 1.80e+00
        pdb=" CG  PHE E  80 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  80 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  80 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  80 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  80 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E  83 "   -0.005 2.00e-02 2.50e+03   1.03e-02 1.05e+00
        pdb=" C   GLY E  83 "    0.018 2.00e-02 2.50e+03
        pdb=" O   GLY E  83 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   PHE E  84 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2722 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3039
        2.77 -     3.30: 15293
        3.30 -     3.84: 28653
        3.84 -     4.37: 34239
        4.37 -     4.90: 55750
  Nonbonded interactions: 136974
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 155 "
            pdb=" NH1 ARG D 168 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OD1 ASP E 155 "
            pdb=" NH1 ARG E 168 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OD1 ASP C 155 "
            pdb=" NH1 ARG C 168 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OD1 ASP A 155 "
            pdb=" NH2 ARG A 168 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OH  TYR E   5 "
            pdb=" O   VAL A 232 "
     model   vdw
     2.288 3.040
  ... (remaining 136969 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ 
h 377 or resid 501))
  selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ 
h 377 or resid 501))
  selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ 
h 377 or resid 501))
  selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ 
h 377 or resid 501))
  selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ 
h 377 or resid 501))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             129.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     47.020
  Find NCS groups from input model:        0.860
  Set up NCS constraints:                  0.100
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  189.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
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      :  0.002   0.035  15905  Z= 0.133
  Angle     :  0.526   7.049  21605  Z= 0.304
  Chirality :  0.036   0.144   2350
  Planarity :  0.003   0.032   2725
  Dihedral  : 14.111  89.927   5690
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  : 10.43 %
    Favored  : 89.51 %
  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:  1.18 (0.18), residues: 1880
  helix:  1.28 (0.14), residues: 1330
  sheet:  None (None), residues: 0
  loop : -0.31 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  93 
 HIS   0.002   0.001   HIS B 115 
 PHE   0.023   0.001   PHE E  80 
 TYR   0.014   0.001   TYR B 284 
 ARG   0.007   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07653 (  981)
  hydrogen bonds       : angle       4.38847 ( 2815)
  covalent geometry    : bond        0.00249 (15905)
  covalent geometry    : angle       0.52639 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 1.823 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7000 (ptp90)
REVERT: E   13 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7042 (ptp90)
REVERT: C   13 ARG cc_start: 0.7362 (ptp90) cc_final: 0.7056 (ptp90)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 1.8121
  time to fit residues: 353.4523
Evaluate side-chains
  170 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 156 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 77 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 168 optimal weight:    0.6980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.090357 restraints weight = 37331.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.18
r_work: 0.2899 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.0519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  15905  Z= 0.154
  Angle     :  0.513   5.381  21605  Z= 0.286
  Chirality :  0.038   0.148   2350
  Planarity :  0.004   0.029   2725
  Dihedral  :  4.213  17.669   2135
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.00 %
    Favored  : 88.48 %
  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:  1.35 (0.18), residues: 1880
  helix:  1.37 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.05 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  93 
 HIS   0.002   0.001   HIS C 156 
 PHE   0.016   0.002   PHE A 171 
 TYR   0.015   0.002   TYR A  97 
 ARG   0.005   0.000   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05944 (  981)
  hydrogen bonds       : angle       4.41722 ( 2815)
  covalent geometry    : bond        0.00325 (15905)
  covalent geometry    : angle       0.51339 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 1.674 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7549 (mtp-110) cc_final: 0.6669 (ptp90)
REVERT: D  172 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.6877 (mp0)
REVERT: D  356 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4395 (ptm160)
REVERT: E   13 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.6676 (ptp90)
REVERT: E   75 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (mp)
REVERT: E  172 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.6829 (mp0)
REVERT: C   13 ARG cc_start: 0.7209 (ptp90) cc_final: 0.6835 (ptp90)
REVERT: C  172 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7052 (mp0)
REVERT: A  172 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.6988 (mp0)
REVERT: B  172 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6780 (mp0)
REVERT: B  356 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4338 (ptm160)
  outliers start: 25
  outliers final: 9
  residues processed: 194
  average time/residue: 1.7509
  time to fit residues: 366.2087
Evaluate side-chains
  195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  172 GLU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 163 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 136 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 133 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
A 173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.115237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.087786 restraints weight = 41923.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.28
r_work: 0.2858 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.0746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  15905  Z= 0.192
  Angle     :  0.550   5.700  21605  Z= 0.305
  Chirality :  0.041   0.158   2350
  Planarity :  0.004   0.047   2725
  Dihedral  :  4.384  18.775   2135
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.55 %
    Favored  : 87.87 %
  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:  1.21 (0.18), residues: 1880
  helix:  1.24 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.04 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  93 
 HIS   0.001   0.001   HIS C 267 
 PHE   0.023   0.002   PHE D  80 
 TYR   0.017   0.002   TYR A  97 
 ARG   0.005   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06528 (  981)
  hydrogen bonds       : angle       4.50208 ( 2815)
  covalent geometry    : bond        0.00427 (15905)
  covalent geometry    : angle       0.55041 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 182
  time to evaluate  : 1.655 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.6684 (ptp90)
REVERT: D  172 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.6883 (mp0)
REVERT: E   13 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.6702 (ptp90)
REVERT: E   75 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6789 (mp)
REVERT: E  172 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6924 (mp0)
REVERT: E  356 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4311 (ptm160)
REVERT: E  375 GLN cc_start: 0.6869 (tp-100) cc_final: 0.6557 (tp40)
REVERT: C   13 ARG cc_start: 0.7182 (ptp90) cc_final: 0.6838 (ptp90)
REVERT: C  172 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7241 (mp0)
REVERT: C  356 ARG cc_start: 0.4764 (OUTLIER) cc_final: 0.4409 (ptm160)
REVERT: A  172 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.6906 (mp0)
REVERT: A  356 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.4396 (ptm160)
REVERT: B  172 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6795 (mp0)
  outliers start: 26
  outliers final: 11
  residues processed: 194
  average time/residue: 1.7462
  time to fit residues: 364.6605
Evaluate side-chains
  196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  100 MET
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  172 GLU
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  172 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 131 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 155 optimal weight:    3.9990
   chunk 179 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 128 optimal weight:    0.1980
   chunk 71 optimal weight:    5.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
A 173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.114395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.087088 restraints weight = 41066.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.26
r_work: 0.2848 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.0856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  15905  Z= 0.215
  Angle     :  0.570   5.833  21605  Z= 0.315
  Chirality :  0.042   0.159   2350
  Planarity :  0.004   0.039   2725
  Dihedral  :  4.488  19.353   2135
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.55 %
    Favored  : 87.74 %
  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:  1.03 (0.18), residues: 1880
  helix:  1.09 (0.14), residues: 1310
  sheet:  None (None), residues: 0
  loop : -0.09 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  93 
 HIS   0.002   0.001   HIS D 267 
 PHE   0.018   0.002   PHE B 188 
 TYR   0.018   0.002   TYR E  97 
 ARG   0.003   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06760 (  981)
  hydrogen bonds       : angle       4.55240 ( 2815)
  covalent geometry    : bond        0.00487 (15905)
  covalent geometry    : angle       0.56999 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 1.938 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6683 (ptp90)
REVERT: D  172 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6908 (mp0)
REVERT: D  356 ARG cc_start: 0.4811 (OUTLIER) cc_final: 0.4338 (ptm160)
REVERT: E   13 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.6725 (ptp90)
REVERT: E   75 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6835 (mp)
REVERT: E  172 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6927 (mp0)
REVERT: E  175 ASN cc_start: 0.8850 (t0) cc_final: 0.8477 (m-40)
REVERT: E  356 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.4377 (ptm160)
REVERT: E  375 GLN cc_start: 0.6845 (tp-100) cc_final: 0.6541 (tp40)
REVERT: C   13 ARG cc_start: 0.7184 (ptp90) cc_final: 0.6860 (ptp90)
REVERT: C  172 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7292 (mp0)
REVERT: C  356 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.4396 (ptm160)
REVERT: A   13 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.6834 (ptp90)
REVERT: A  172 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.6910 (mp0)
REVERT: A  356 ARG cc_start: 0.4958 (OUTLIER) cc_final: 0.4428 (ptm160)
REVERT: B  172 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6816 (mp0)
REVERT: B  356 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.4311 (ptm160)
  outliers start: 28
  outliers final: 11
  residues processed: 192
  average time/residue: 1.7911
  time to fit residues: 370.4763
Evaluate side-chains
  196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  100 MET
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  172 GLU
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0670
   chunk 11 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 164 optimal weight:    0.8980
   chunk 109 optimal weight:    7.9990
   chunk 148 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 167 optimal weight:    1.9990
   overall best weight:    1.0722

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.116984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.089785 restraints weight = 40876.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.26
r_work: 0.2889 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2771
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2771 r_free = 0.2771    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2771 r_free = 0.2771    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2771
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.0723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15905  Z= 0.141
  Angle     :  0.496   5.599  21605  Z= 0.278
  Chirality :  0.037   0.152   2350
  Planarity :  0.003   0.035   2725
  Dihedral  :  4.242  17.522   2135
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.49 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.18), residues: 1880
  helix:  1.30 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.06 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  93 
 HIS   0.002   0.001   HIS E 115 
 PHE   0.021   0.002   PHE E  80 
 TYR   0.014   0.001   TYR A  97 
 ARG   0.003   0.000   ARG D 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05833 (  981)
  hydrogen bonds       : angle       4.41443 ( 2815)
  covalent geometry    : bond        0.00291 (15905)
  covalent geometry    : angle       0.49637 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 1.748 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.6694 (ptp90)
REVERT: D   75 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6871 (pp)
REVERT: D  172 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6865 (mp0)
REVERT: D  356 ARG cc_start: 0.4713 (OUTLIER) cc_final: 0.4322 (ptm160)
REVERT: E   13 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6692 (ptp90)
REVERT: E   75 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6835 (mp)
REVERT: E  172 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8080 (mp0)
REVERT: E  175 ASN cc_start: 0.8821 (t0) cc_final: 0.8447 (m-40)
REVERT: E  356 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.4326 (ptm160)
REVERT: C   13 ARG cc_start: 0.7105 (ptp90) cc_final: 0.6798 (ptp90)
REVERT: C  172 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7167 (mp0)
REVERT: C  356 ARG cc_start: 0.4778 (OUTLIER) cc_final: 0.4393 (ptm160)
REVERT: A   13 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6788 (ptp90)
REVERT: A  172 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.6815 (mp0)
REVERT: A  356 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.4366 (ptm160)
REVERT: B   13 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6454 (ptp90)
REVERT: B  172 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6700 (mp0)
REVERT: B  356 ARG cc_start: 0.4815 (OUTLIER) cc_final: 0.4334 (ptm160)
  outliers start: 28
  outliers final: 9
  residues processed: 192
  average time/residue: 1.8063
  time to fit residues: 373.0678
Evaluate side-chains
  197 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 1.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  172 GLU
Chi-restraints excluded: chain E residue  197 ARG
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 156 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 162 optimal weight:    4.9990
   chunk 172 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.113663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.086302 restraints weight = 43302.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.30
r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  15905  Z= 0.252
  Angle     :  0.594   6.418  21605  Z= 0.328
  Chirality :  0.044   0.161   2350
  Planarity :  0.005   0.042   2725
  Dihedral  :  4.542  19.812   2135
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.24 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.18), residues: 1880
  helix:  1.05 (0.14), residues: 1310
  sheet:  None (None), residues: 0
  loop : -0.09 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  93 
 HIS   0.002   0.001   HIS B 226 
 PHE   0.020   0.003   PHE A 188 
 TYR   0.020   0.002   TYR A  97 
 ARG   0.004   0.001   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07047 (  981)
  hydrogen bonds       : angle       4.59534 ( 2815)
  covalent geometry    : bond        0.00579 (15905)
  covalent geometry    : angle       0.59449 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.648 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.6714 (ptp90)
REVERT: D   75 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6970 (pp)
REVERT: D  172 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: D  356 ARG cc_start: 0.4807 (OUTLIER) cc_final: 0.4335 (ptm160)
REVERT: E   13 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.6755 (ptp90)
REVERT: E   75 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6893 (mp)
REVERT: E  172 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7000 (mp0)
REVERT: E  356 ARG cc_start: 0.4936 (OUTLIER) cc_final: 0.4408 (ptm160)
REVERT: C   13 ARG cc_start: 0.7205 (ptp90) cc_final: 0.6909 (ptp90)
REVERT: C  172 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7378 (mp0)
REVERT: C  356 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.4435 (ptm160)
REVERT: A   13 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.6781 (ptp90)
REVERT: A  172 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.6899 (mp0)
REVERT: A  356 ARG cc_start: 0.4939 (OUTLIER) cc_final: 0.4390 (ptm160)
REVERT: B  165 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7880 (mtt90)
REVERT: B  172 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6798 (mp0)
REVERT: B  356 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.4445 (ptm160)
  outliers start: 32
  outliers final: 12
  residues processed: 192
  average time/residue: 1.8320
  time to fit residues: 378.4806
Evaluate side-chains
  201 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  100 MET
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  172 GLU
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  165 ARG
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 121 optimal weight:    0.4980
   chunk 129 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 161 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 139 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.117665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.090345 restraints weight = 44085.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.34
r_work: 0.2897 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.0739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  15905  Z= 0.129
  Angle     :  0.486   5.661  21605  Z= 0.272
  Chirality :  0.037   0.151   2350
  Planarity :  0.003   0.037   2725
  Dihedral  :  4.187  16.945   2135
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.10 %
    Favored  : 87.50 %
  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:  1.29 (0.18), residues: 1880
  helix:  1.34 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.10 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  93 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.023   0.002   PHE C  80 
 TYR   0.013   0.001   TYR A  97 
 ARG   0.003   0.000   ARG E 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05597 (  981)
  hydrogen bonds       : angle       4.38507 ( 2815)
  covalent geometry    : bond        0.00257 (15905)
  covalent geometry    : angle       0.48578 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 1.641 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7526 (mtp-110) cc_final: 0.6672 (ptp90)
REVERT: D   75 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6849 (pp)
REVERT: D  172 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6832 (mp0)
REVERT: D  356 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.4271 (ptm160)
REVERT: E   13 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.6661 (ptp90)
REVERT: E  175 ASN cc_start: 0.8810 (t0) cc_final: 0.8416 (m-40)
REVERT: E  356 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.4323 (ptm160)
REVERT: C   13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6950 (ptp90)
REVERT: C  172 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7199 (mp0)
REVERT: C  356 ARG cc_start: 0.4702 (OUTLIER) cc_final: 0.4359 (ptm160)
REVERT: A   13 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6765 (ptp90)
REVERT: A  172 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6779 (mp0)
REVERT: A  356 ARG cc_start: 0.4789 (OUTLIER) cc_final: 0.4348 (ptm160)
REVERT: B   13 ARG cc_start: 0.7424 (mtp-110) cc_final: 0.6475 (ptp90)
REVERT: B  172 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.6679 (mp0)
REVERT: B  356 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.4342 (ptm160)
REVERT: B  374 MET cc_start: 0.6413 (mtm) cc_final: 0.6121 (mtm)
  outliers start: 23
  outliers final: 8
  residues processed: 189
  average time/residue: 1.8230
  time to fit residues: 370.8229
Evaluate side-chains
  192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  197 ARG
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 173 optimal weight:    5.9990
   chunk 175 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0070
   chunk 58 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 177 optimal weight:    1.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.091550 restraints weight = 42690.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.31
r_work: 0.2916 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15905  Z= 0.122
  Angle     :  0.472   5.965  21605  Z= 0.264
  Chirality :  0.036   0.149   2350
  Planarity :  0.003   0.034   2725
  Dihedral  :  4.045  16.119   2135
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.10 %
    Favored  : 87.68 %
  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:  1.40 (0.18), residues: 1880
  helix:  1.43 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.10 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  93 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.027   0.001   PHE A 283 
 TYR   0.014   0.001   TYR A  97 
 ARG   0.007   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05388 (  981)
  hydrogen bonds       : angle       4.34109 ( 2815)
  covalent geometry    : bond        0.00240 (15905)
  covalent geometry    : angle       0.47201 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 1.763 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.6665 (ptp90)
REVERT: D   75 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6881 (pp)
REVERT: D  356 ARG cc_start: 0.4620 (OUTLIER) cc_final: 0.4258 (ptm160)
REVERT: E   13 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.6637 (ptp90)
REVERT: E  175 ASN cc_start: 0.8775 (t0) cc_final: 0.8378 (m-40)
REVERT: E  356 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.4275 (ptm160)
REVERT: C   13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6832 (ptt90)
REVERT: C   44 MET cc_start: 0.8900 (mmt) cc_final: 0.8678 (mmm)
REVERT: C  172 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7109 (mp0)
REVERT: C  356 ARG cc_start: 0.4745 (OUTLIER) cc_final: 0.4388 (ptm160)
REVERT: A   13 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.6708 (ptp90)
REVERT: A  172 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.6789 (mp0)
REVERT: A  356 ARG cc_start: 0.4767 (OUTLIER) cc_final: 0.4330 (ptm160)
REVERT: B   13 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6534 (ptp90)
REVERT: B  172 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.6705 (mp0)
REVERT: B  356 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.4294 (ptm160)
REVERT: B  374 MET cc_start: 0.6374 (mtm) cc_final: 0.6105 (mtm)
  outliers start: 20
  outliers final: 7
  residues processed: 189
  average time/residue: 1.8981
  time to fit residues: 386.3338
Evaluate side-chains
  192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 176
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  197 ARG
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 180 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 167 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 153 optimal weight:    0.5980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.088187 restraints weight = 39044.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.22
r_work: 0.2867 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.0859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15905  Z= 0.188
  Angle     :  0.542   6.238  21605  Z= 0.300
  Chirality :  0.040   0.157   2350
  Planarity :  0.004   0.037   2725
  Dihedral  :  4.320  18.292   2135
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.22 %
    Favored  : 87.56 %
  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:  1.25 (0.18), residues: 1880
  helix:  1.29 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.06 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  93 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.030   0.002   PHE C  80 
 TYR   0.018   0.002   TYR A  97 
 ARG   0.005   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06394 (  981)
  hydrogen bonds       : angle       4.48294 ( 2815)
  covalent geometry    : bond        0.00417 (15905)
  covalent geometry    : angle       0.54152 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 2.047 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.6739 (ptp90)
REVERT: D   75 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6922 (pp)
REVERT: D  356 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.4301 (ptm160)
REVERT: E   13 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6712 (ptp90)
REVERT: E  175 ASN cc_start: 0.8848 (t0) cc_final: 0.8473 (m-40)
REVERT: E  356 ARG cc_start: 0.4723 (OUTLIER) cc_final: 0.4322 (ptm160)
REVERT: C   13 ARG cc_start: 0.7225 (ptp90) cc_final: 0.7025 (ptp90)
REVERT: C  172 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7274 (mp0)
REVERT: C  356 ARG cc_start: 0.4755 (OUTLIER) cc_final: 0.4367 (ptm160)
REVERT: A   13 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6772 (ptp90)
REVERT: A  172 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.6871 (mp0)
REVERT: A  356 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.4373 (ptm160)
REVERT: B   13 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6576 (ptp90)
REVERT: B  172 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6788 (mp0)
REVERT: B  356 ARG cc_start: 0.4847 (OUTLIER) cc_final: 0.4357 (ptm160)
REVERT: B  374 MET cc_start: 0.6435 (mtm) cc_final: 0.6151 (mtm)
  outliers start: 20
  outliers final: 8
  residues processed: 190
  average time/residue: 1.9148
  time to fit residues: 391.6631
Evaluate side-chains
  192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 182 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
E  71 GLN
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.118468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.091255 restraints weight = 41455.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.28
r_work: 0.2912 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.0771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  15905  Z= 0.124
  Angle     :  0.478   5.766  21605  Z= 0.267
  Chirality :  0.036   0.149   2350
  Planarity :  0.003   0.053   2725
  Dihedral  :  4.086  16.094   2135
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.34 %
    Favored  : 87.56 %
  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:  1.39 (0.18), residues: 1880
  helix:  1.42 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.09 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  93 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.023   0.001   PHE A 283 
 TYR   0.013   0.001   TYR A  97 
 ARG   0.006   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05440 (  981)
  hydrogen bonds       : angle       4.35780 ( 2815)
  covalent geometry    : bond        0.00245 (15905)
  covalent geometry    : angle       0.47805 (21605)

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

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

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3760 Ramachandran restraints generated.
    1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 1.713 
Fit side-chains
REVERT: D   13 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.6644 (ptp90)
REVERT: D   75 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6883 (pp)
REVERT: D  356 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.4247 (ptm160)
REVERT: E   13 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.6641 (ptp90)
REVERT: E  175 ASN cc_start: 0.8789 (t0) cc_final: 0.8417 (m-40)
REVERT: E  356 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4264 (ptm160)
REVERT: C   13 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6837 (ptp90)
REVERT: C   44 MET cc_start: 0.8903 (mmt) cc_final: 0.8675 (mmt)
REVERT: C  172 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7130 (mp0)
REVERT: C  356 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4389 (ptm160)
REVERT: A   13 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.6705 (ptp90)
REVERT: A  172 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.6778 (mp0)
REVERT: A  356 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4311 (ptm160)
REVERT: B   13 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6544 (ptp90)
REVERT: B  172 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6630 (mp0)
REVERT: B  356 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.4297 (ptm160)
REVERT: B  374 MET cc_start: 0.6383 (mtm) cc_final: 0.6115 (mtm)
  outliers start: 18
  outliers final: 7
  residues processed: 187
  average time/residue: 1.8195
  time to fit residues: 366.0184
Evaluate side-chains
  191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  356 ARG
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  356 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  100 MET
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  356 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  356 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 165 optimal weight:    2.9990
   chunk 164 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9980
   chunk 127 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 93 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 173 ASN
A  19 GLN
A 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.091877 restraints weight = 38017.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.20
r_work: 0.2923 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  15905  Z= 0.124
  Angle     :  0.475   6.145  21605  Z= 0.266
  Chirality :  0.036   0.149   2350
  Planarity :  0.003   0.053   2725
  Dihedral  :  4.024  16.044   2135
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.59 %
    Favored  : 87.44 %
  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:  1.44 (0.18), residues: 1880
  helix:  1.47 (0.14), residues: 1300
  sheet:  None (None), residues: 0
  loop : -0.10 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  93 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.030   0.002   PHE E  80 
 TYR   0.014   0.001   TYR A  97 
 ARG   0.007   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05410 (  981)
  hydrogen bonds       : angle       4.33043 ( 2815)
  covalent geometry    : bond        0.00247 (15905)
  covalent geometry    : angle       0.47522 (21605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15318.84 seconds
wall clock time: 264 minutes 26.54 seconds (15866.54 seconds total)