Starting phenix.real_space_refine
on Tue Mar  3 22:46:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2026/7uxu_26862.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.051
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
     P       8      5.49       5
     S       8      5.16       5
     C    2852      2.51       5
     N     744      2.21       5
     O     896      1.98       5
     H    4268      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8776
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2148
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 3, 'TRANS': 130}
    Chain: "B"
      Number of atoms: 2148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2148
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 3, 'TRANS': 130}
    Chain: "C"
      Number of atoms: 2148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2148
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 3, 'TRANS': 130}
    Chain: "D"
      Number of atoms: 2148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 2148
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 3, 'TRANS': 130}
    Chain: "A"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'1O4': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'1O4': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'1O4': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'1O4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.41, per 1000 atoms: 0.16
  Number of scatterers: 8776
  At special positions: 0
  Unit cell: (77.6, 64, 111.2, 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)
     S       8     16.00
     P       8     15.00
     O     896      8.00
     N     744      7.00
     C    2852      6.00
     H    4268      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 198.7 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1024

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      64.9% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.580A  pdb=" N   LYS A 146 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 161
    Processing helix  chain 'A' and resid 166 through 171
    Processing helix  chain 'A' and resid 176 through 187
    Processing helix  chain 'A' and resid 196 through 202
      removed outlier: 3.956A  pdb=" N   LYS A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 217
      removed outlier: 3.841A  pdb=" N   ASN A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY A 211 " --> pdb=" O   TYR A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.820A  pdb=" N   VAL A 265 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.574A  pdb=" N   LYS B 146 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 161
    Processing helix  chain 'B' and resid 166 through 171
    Processing helix  chain 'B' and resid 176 through 187
    Processing helix  chain 'B' and resid 196 through 202
      removed outlier: 4.009A  pdb=" N   LYS B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 217
      removed outlier: 3.918A  pdb=" N   ASN B 206 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY B 211 " --> pdb=" O   TYR B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 239
    Processing helix  chain 'B' and resid 241 through 245
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.768A  pdb=" N   VAL B 265 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 146
      removed outlier: 3.596A  pdb=" N   LYS C 146 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 161
    Processing helix  chain 'C' and resid 166 through 171
    Processing helix  chain 'C' and resid 176 through 187
    Processing helix  chain 'C' and resid 196 through 202
      removed outlier: 4.068A  pdb=" N   LYS C 201 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.913A  pdb=" N   ASN C 206 " --> pdb=" O   LYS C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 239
    Processing helix  chain 'C' and resid 241 through 245
    Processing helix  chain 'C' and resid 254 through 267
      removed outlier: 3.783A  pdb=" N   VAL C 265 " --> pdb=" O   GLN C 261 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
      removed outlier: 3.641A  pdb=" N   LYS D 146 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 161
    Processing helix  chain 'D' and resid 166 through 171
    Processing helix  chain 'D' and resid 176 through 187
    Processing helix  chain 'D' and resid 196 through 202
      removed outlier: 4.009A  pdb=" N   LYS D 201 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS D 202 " --> pdb=" O   ASP D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
      removed outlier: 3.901A  pdb=" N   ASN D 206 " --> pdb=" O   LYS D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 239
    Processing helix  chain 'D' and resid 241 through 245
    Processing helix  chain 'D' and resid 254 through 267
      removed outlier: 3.810A  pdb=" N   VAL D 265 " --> pdb=" O   GLN D 261 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 165
      removed outlier: 6.900A  pdb=" N   LEU A 137 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   PHE A 138 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   VAL A 194 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   SER A 140 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165
      removed outlier: 6.876A  pdb=" N   LEU B 137 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   PHE B 138 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   VAL B 194 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   SER B 140 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL B 193 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 164 through 165
      removed outlier: 6.872A  pdb=" N   LEU C 137 " --> pdb=" O   TRP C 165 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   PHE C 138 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   VAL C 194 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   SER C 140 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL C 193 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 164 through 165
      removed outlier: 6.874A  pdb=" N   LEU D 137 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   PHE D 138 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   VAL D 194 " --> pdb=" O   PHE D 138 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   SER D 140 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL D 193 " --> pdb=" O   LEU D 224 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    585 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: 1.69

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4268
        1.03 -     1.22: 4
        1.22 -     1.42: 1936
        1.42 -     1.61: 2656
        1.61 -     1.80: 16
  Bond restraints: 8880
  Sorted by residual:
  bond pdb=" O1  1O4 A 301 "
       pdb=" P   1O4 A 301 "
    ideal  model  delta    sigma   weight residual
    1.656  1.599  0.057 2.00e-02 2.50e+03 8.16e+00
  bond pdb=" O1  1O4 C 301 "
       pdb=" P   1O4 C 301 "
    ideal  model  delta    sigma   weight residual
    1.656  1.600  0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" O1  1O4 D 301 "
       pdb=" P   1O4 D 301 "
    ideal  model  delta    sigma   weight residual
    1.656  1.600  0.056 2.00e-02 2.50e+03 7.82e+00
  bond pdb=" O1  1O4 B 301 "
       pdb=" P   1O4 B 301 "
    ideal  model  delta    sigma   weight residual
    1.656  1.600  0.056 2.00e-02 2.50e+03 7.77e+00
  bond pdb=" O   1O4 B 301 "
       pdb=" P   1O4 B 301 "
    ideal  model  delta    sigma   weight residual
    1.647  1.593  0.054 2.00e-02 2.50e+03 7.41e+00
  ... (remaining 8875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 15575
        1.87 -     3.74: 383
        3.74 -     5.62: 45
        5.62 -     7.49: 9
        7.49 -     9.36: 4
  Bond angle restraints: 16016
  Sorted by residual:
  angle pdb=" O   1O4 C 301 "
        pdb=" P   1O4 C 301 "
        pdb=" O1  1O4 C 301 "
      ideal   model   delta    sigma   weight residual
      96.18  105.54   -9.36 3.00e+00 1.11e-01 9.74e+00
  angle pdb=" N   PRO A 225 "
        pdb=" CA  PRO A 225 "
        pdb=" C   PRO A 225 "
      ideal   model   delta    sigma   weight residual
     111.68  116.75   -5.07 1.67e+00 3.59e-01 9.23e+00
  angle pdb=" O   1O4 A 301 "
        pdb=" P   1O4 A 301 "
        pdb=" O1  1O4 A 301 "
      ideal   model   delta    sigma   weight residual
      96.18  105.09   -8.91 3.00e+00 1.11e-01 8.81e+00
  angle pdb=" N   PRO C 225 "
        pdb=" CA  PRO C 225 "
        pdb=" C   PRO C 225 "
      ideal   model   delta    sigma   weight residual
     111.68  116.51   -4.83 1.67e+00 3.59e-01 8.36e+00
  angle pdb=" O   1O4 D 301 "
        pdb=" P   1O4 D 301 "
        pdb=" O1  1O4 D 301 "
      ideal   model   delta    sigma   weight residual
      96.18  104.75   -8.57 3.00e+00 1.11e-01 8.16e+00
  ... (remaining 16011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.56: 3847
       16.56 -    33.12: 245
       33.12 -    49.68: 107
       49.68 -    66.24: 62
       66.24 -    82.80: 11
  Dihedral angle restraints: 4272
    sinusoidal: 2416
      harmonic: 1856
  Sorted by residual:
  dihedral pdb=" CA  MET B 222 "
           pdb=" C   MET B 222 "
           pdb=" N   ILE B 223 "
           pdb=" CA  ILE B 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.06  -23.94     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  MET D 222 "
           pdb=" C   MET D 222 "
           pdb=" N   ILE D 223 "
           pdb=" CA  ILE D 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.29  -23.71     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  MET C 222 "
           pdb=" C   MET C 222 "
           pdb=" N   ILE C 223 "
           pdb=" CA  ILE C 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.40  -23.60     0      5.00e+00 4.00e-02 2.23e+01
  ... (remaining 4269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 432
       0.043 -    0.085: 215
       0.085 -    0.128: 41
       0.128 -    0.171: 20
       0.171 -    0.214: 8
  Chirality restraints: 716
  Sorted by residual:
  chirality pdb=" C1  1O4 C 301 "
            pdb=" C   1O4 C 301 "
            pdb=" C2  1O4 C 301 "
            pdb=" O12 1O4 C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.70    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C1  1O4 B 301 "
            pdb=" C   1O4 B 301 "
            pdb=" C2  1O4 B 301 "
            pdb=" O12 1O4 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.70    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C1  1O4 A 301 "
            pdb=" C   1O4 A 301 "
            pdb=" C2  1O4 A 301 "
            pdb=" O12 1O4 A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.70    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 713 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   1O4 B 301 "   -0.369 2.00e-02 2.50e+03   1.47e-01 6.53e+02
        pdb=" C15 1O4 B 301 "    0.121 2.00e-02 2.50e+03
        pdb=" C16 1O4 B 301 "    0.089 2.00e-02 2.50e+03
        pdb=" C17 1O4 B 301 "    0.035 2.00e-02 2.50e+03
        pdb=" C18 1O4 B 301 "   -0.111 2.00e-02 2.50e+03
        pdb=" C19 1O4 B 301 "   -0.171 2.00e-02 2.50e+03
        pdb=" C20 1O4 B 301 "   -0.073 2.00e-02 2.50e+03
        pdb=" C21 1O4 B 301 "    0.052 2.00e-02 2.50e+03
        pdb=" C22 1O4 B 301 "    0.110 2.00e-02 2.50e+03
        pdb=" C23 1O4 B 301 "    0.153 2.00e-02 2.50e+03
        pdb=" N5  1O4 B 301 "    0.047 2.00e-02 2.50e+03
        pdb=" N6  1O4 B 301 "    0.117 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   1O4 C 301 "    0.351 2.00e-02 2.50e+03   1.41e-01 5.94e+02
        pdb=" C15 1O4 C 301 "   -0.111 2.00e-02 2.50e+03
        pdb=" C16 1O4 C 301 "   -0.085 2.00e-02 2.50e+03
        pdb=" C17 1O4 C 301 "   -0.034 2.00e-02 2.50e+03
        pdb=" C18 1O4 C 301 "    0.108 2.00e-02 2.50e+03
        pdb=" C19 1O4 C 301 "    0.164 2.00e-02 2.50e+03
        pdb=" C20 1O4 C 301 "    0.070 2.00e-02 2.50e+03
        pdb=" C21 1O4 C 301 "   -0.052 2.00e-02 2.50e+03
        pdb=" C22 1O4 C 301 "   -0.106 2.00e-02 2.50e+03
        pdb=" C23 1O4 C 301 "   -0.145 2.00e-02 2.50e+03
        pdb=" N5  1O4 C 301 "   -0.045 2.00e-02 2.50e+03
        pdb=" N6  1O4 C 301 "   -0.115 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   1O4 A 301 "   -0.347 2.00e-02 2.50e+03   1.39e-01 5.81e+02
        pdb=" C15 1O4 A 301 "    0.104 2.00e-02 2.50e+03
        pdb=" C16 1O4 A 301 "    0.082 2.00e-02 2.50e+03
        pdb=" C17 1O4 A 301 "    0.034 2.00e-02 2.50e+03
        pdb=" C18 1O4 A 301 "   -0.107 2.00e-02 2.50e+03
        pdb=" C19 1O4 A 301 "   -0.163 2.00e-02 2.50e+03
        pdb=" C20 1O4 A 301 "   -0.068 2.00e-02 2.50e+03
        pdb=" C21 1O4 A 301 "    0.051 2.00e-02 2.50e+03
        pdb=" C22 1O4 A 301 "    0.105 2.00e-02 2.50e+03
        pdb=" C23 1O4 A 301 "    0.146 2.00e-02 2.50e+03
        pdb=" N5  1O4 A 301 "    0.046 2.00e-02 2.50e+03
        pdb=" N6  1O4 A 301 "    0.117 2.00e-02 2.50e+03
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 920
        2.27 -     2.85: 18795
        2.85 -     3.43: 20434
        3.43 -     4.02: 29483
        4.02 -     4.60: 45114
  Nonbonded interactions: 114746
  Sorted by model distance:
  nonbonded pdb=" HG  SER A 140 "
            pdb=" OE1 GLU A 208 "
     model   vdw
     1.686 2.450
  nonbonded pdb=" HG  SER B 140 "
            pdb=" OE1 GLU B 208 "
     model   vdw
     1.696 2.450
  nonbonded pdb=" HG  SER C 140 "
            pdb=" OE1 GLU C 208 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" HG  SER D 140 "
            pdb=" OE1 GLU D 208 "
     model   vdw
     1.732 2.450
  nonbonded pdb=" HE  ARG A 178 "
            pdb=" OD1 ASP C 210 "
     model   vdw
     1.790 2.450
  ... (remaining 114741 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.150
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
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      :  0.007   0.057   4612  Z= 0.328
  Angle     :  1.006   9.361   6292  Z= 0.565
  Chirality :  0.056   0.214    716
  Planarity :  0.013   0.147    768
  Dihedral  : 17.352  82.799   1844
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.34), residues: 528
  helix: -0.82 (0.28), residues: 256
  sheet: -0.19 (0.47), residues: 84
  loop :  0.82 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 178 
 TYR   0.018   0.004   TYR D 238 
 PHE   0.019   0.003   PHE C 138 
 TRP   0.017   0.003   TRP C 204 
 HIS   0.007   0.003   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 4612)
  covalent geometry    : angle       1.00595 ( 6292)
  hydrogen bonds       : bond        0.28998 (  211)
  hydrogen bonds       : angle       6.50920 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  189 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7524 (mtmt)
REVERT: A  222 MET cc_start: 0.8702 (mtp) cc_final: 0.8451 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 1.3366
  time to fit residues: 90.9157
Evaluate side-chains
  48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
B 249 ASN
C 249 ASN
D 249 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.104158 restraints weight = 16773.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.58
r_work: 0.3191 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4612  Z= 0.137
  Angle     :  0.564   4.953   6292  Z= 0.307
  Chirality :  0.041   0.143    716
  Planarity :  0.005   0.040    768
  Dihedral  : 12.973  69.834    800
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 0.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.85 %
    Favored  : 91.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.34), residues: 528
  helix:  0.75 (0.31), residues: 248
  sheet: -0.88 (0.45), residues: 84
  loop :  0.52 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.013   0.002   TYR D 207 
 PHE   0.008   0.002   PHE C 138 
 TRP   0.009   0.001   TRP C 204 
 HIS   0.004   0.001   HIS C 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4612)
  covalent geometry    : angle       0.56395 ( 6292)
  hydrogen bonds       : bond        0.05995 (  211)
  hydrogen bonds       : angle       4.14054 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  189 LYS cc_start: 0.7610 (mmmm) cc_final: 0.7231 (ttmt)
REVERT: A  216 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7511 (tt0)
REVERT: A  222 MET cc_start: 0.8484 (mtp) cc_final: 0.8226 (mtp)
REVERT: B  216 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7524 (tt0)
REVERT: C  189 LYS cc_start: 0.7756 (mttt) cc_final: 0.7204 (ttmt)
  outliers start: 4
  outliers final: 1
  residues processed: 49
  average time/residue: 1.2735
  time to fit residues: 64.5819
Evaluate side-chains
  43 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain B residue  216 GLU
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 249 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.117565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.106966 restraints weight = 16769.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.52
r_work: 0.3238 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4612  Z= 0.113
  Angle     :  0.491   4.157   6292  Z= 0.267
  Chirality :  0.039   0.138    716
  Planarity :  0.004   0.044    768
  Dihedral  : 12.249  66.738    800
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.30 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.35), residues: 528
  helix:  1.37 (0.33), residues: 248
  sheet: -1.49 (0.44), residues: 84
  loop :  0.32 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 215 
 TYR   0.012   0.002   TYR D 207 
 PHE   0.007   0.001   PHE A 138 
 TRP   0.005   0.001   TRP C 204 
 HIS   0.003   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4612)
  covalent geometry    : angle       0.49069 ( 6292)
  hydrogen bonds       : bond        0.04997 (  211)
  hydrogen bonds       : angle       3.88888 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6348 (mp0)
REVERT: A  189 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7308 (ttmt)
REVERT: C  189 LYS cc_start: 0.7808 (mttt) cc_final: 0.7189 (mtmt)
  outliers start: 6
  outliers final: 1
  residues processed: 48
  average time/residue: 1.2662
  time to fit residues: 62.9347
Evaluate side-chains
  41 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
B 249 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.105602 restraints weight = 16928.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.52
r_work: 0.3217 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4612  Z= 0.123
  Angle     :  0.506   4.226   6292  Z= 0.274
  Chirality :  0.040   0.140    716
  Planarity :  0.005   0.047    768
  Dihedral  : 12.361  68.659    800
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.12 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.35), residues: 528
  helix:  1.51 (0.33), residues: 248
  sheet: -1.83 (0.44), residues: 84
  loop :  0.10 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 215 
 TYR   0.012   0.002   TYR D 207 
 PHE   0.008   0.001   PHE B 138 
 TRP   0.005   0.001   TRP C 204 
 HIS   0.003   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4612)
  covalent geometry    : angle       0.50563 ( 6292)
  hydrogen bonds       : bond        0.05253 (  211)
  hydrogen bonds       : angle       3.84994 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6483 (mp0)
REVERT: A  189 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7398 (ttmt)
REVERT: C  189 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7325 (ttmt)
  outliers start: 6
  outliers final: 2
  residues processed: 46
  average time/residue: 1.1935
  time to fit residues: 56.9145
Evaluate side-chains
  44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.115973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.105497 restraints weight = 16825.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.51
r_work: 0.3216 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4612  Z= 0.118
  Angle     :  0.494   4.125   6292  Z= 0.267
  Chirality :  0.040   0.138    716
  Planarity :  0.005   0.047    768
  Dihedral  : 12.257  68.658    800
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 11.16 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.36), residues: 528
  helix:  1.70 (0.33), residues: 248
  sheet: -1.98 (0.45), residues: 84
  loop : -0.01 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 215 
 TYR   0.012   0.001   TYR D 207 
 PHE   0.008   0.001   PHE B 138 
 TRP   0.006   0.001   TRP C 204 
 HIS   0.003   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4612)
  covalent geometry    : angle       0.49433 ( 6292)
  hydrogen bonds       : bond        0.04993 (  211)
  hydrogen bonds       : angle       3.80380 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6491 (mp0)
REVERT: A  189 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7460 (ttmt)
REVERT: C  189 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7349 (ttmt)
  outliers start: 2
  outliers final: 2
  residues processed: 44
  average time/residue: 1.2001
  time to fit residues: 54.8706
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain C residue  264 ASP
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.121188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.111734 restraints weight = 16931.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.33
r_work: 0.3284 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4612  Z= 0.104
  Angle     :  0.464   3.831   6292  Z= 0.250
  Chirality :  0.039   0.136    716
  Planarity :  0.004   0.045    768
  Dihedral  : 11.864  66.888    800
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.16 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.36), residues: 528
  helix:  1.96 (0.33), residues: 248
  sheet: -1.98 (0.46), residues: 84
  loop :  0.02 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 215 
 TYR   0.012   0.001   TYR D 207 
 PHE   0.006   0.001   PHE A 138 
 TRP   0.005   0.001   TRP C 204 
 HIS   0.002   0.001   HIS D 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 4612)
  covalent geometry    : angle       0.46413 ( 6292)
  hydrogen bonds       : bond        0.04374 (  211)
  hydrogen bonds       : angle       3.73367 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6582 (mp0)
REVERT: A  189 LYS cc_start: 0.7880 (mmmm) cc_final: 0.7501 (ttmt)
REVERT: C  189 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7411 (ttmt)
REVERT: D  189 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7368 (tttt)
  outliers start: 3
  outliers final: 1
  residues processed: 42
  average time/residue: 1.2937
  time to fit residues: 56.3039
Evaluate side-chains
  44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.108892 restraints weight = 17186.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.30
r_work: 0.3239 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4612  Z= 0.149
  Angle     :  0.548   4.100   6292  Z= 0.291
  Chirality :  0.041   0.142    716
  Planarity :  0.005   0.050    768
  Dihedral  : 12.768  71.123    800
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 12.40 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.35), residues: 528
  helix:  1.60 (0.32), residues: 248
  sheet: -2.15 (0.46), residues: 84
  loop : -0.01 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 215 
 TYR   0.012   0.002   TYR C 207 
 PHE   0.009   0.002   PHE B 138 
 TRP   0.006   0.001   TRP C 204 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4612)
  covalent geometry    : angle       0.54760 ( 6292)
  hydrogen bonds       : bond        0.05954 (  211)
  hydrogen bonds       : angle       3.83325 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  189 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7536 (ttmt)
REVERT: C  189 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7421 (mtmt)
REVERT: D  189 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7371 (tttt)
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 1.2854
  time to fit residues: 57.2499
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110715 restraints weight = 16767.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.28
r_work: 0.3273 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4612  Z= 0.143
  Angle     :  0.540   4.084   6292  Z= 0.287
  Chirality :  0.041   0.141    716
  Planarity :  0.005   0.050    768
  Dihedral  : 12.714  70.367    800
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 13.22 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.35), residues: 528
  helix:  1.56 (0.32), residues: 248
  sheet: -2.23 (0.46), residues: 84
  loop : -0.05 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 215 
 TYR   0.012   0.002   TYR D 207 
 PHE   0.009   0.002   PHE D 138 
 TRP   0.006   0.001   TRP C 204 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4612)
  covalent geometry    : angle       0.54040 ( 6292)
  hydrogen bonds       : bond        0.05739 (  211)
  hydrogen bonds       : angle       3.83779 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6612 (mp0)
REVERT: A  189 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7567 (ttmt)
REVERT: C  189 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7439 (mtmt)
REVERT: D  189 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7370 (tttt)
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 1.2621
  time to fit residues: 56.2754
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.7188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.110958 restraints weight = 16670.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.29
r_work: 0.3279 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4612  Z= 0.136
  Angle     :  0.529   4.115   6292  Z= 0.281
  Chirality :  0.041   0.141    716
  Planarity :  0.005   0.050    768
  Dihedral  : 12.599  69.778    800
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 13.22 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.35), residues: 528
  helix:  1.62 (0.32), residues: 248
  sheet: -2.23 (0.46), residues: 84
  loop : -0.03 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 215 
 TYR   0.012   0.002   TYR C 207 
 PHE   0.008   0.001   PHE B 138 
 TRP   0.006   0.001   TRP C 204 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4612)
  covalent geometry    : angle       0.52919 ( 6292)
  hydrogen bonds       : bond        0.05548 (  211)
  hydrogen bonds       : angle       3.82684 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6615 (mp0)
REVERT: A  189 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7582 (ttmt)
REVERT: C  189 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7461 (mtmt)
REVERT: D  189 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7377 (tttt)
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 1.2596
  time to fit residues: 56.1515
Evaluate side-chains
  44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.119384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110052 restraints weight = 16798.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.29
r_work: 0.3265 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4612  Z= 0.151
  Angle     :  0.557   4.181   6292  Z= 0.295
  Chirality :  0.041   0.143    716
  Planarity :  0.005   0.051    768
  Dihedral  : 12.895  71.270    800
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 0.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 13.02 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.35), residues: 528
  helix:  1.48 (0.32), residues: 248
  sheet: -2.27 (0.46), residues: 84
  loop : -0.11 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 215 
 TYR   0.012   0.002   TYR C 207 
 PHE   0.009   0.002   PHE D 138 
 TRP   0.006   0.001   TRP C 204 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4612)
  covalent geometry    : angle       0.55681 ( 6292)
  hydrogen bonds       : bond        0.06057 (  211)
  hydrogen bonds       : angle       3.87228 (  585)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6632 (mp0)
REVERT: A  189 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7593 (ttmt)
REVERT: C  189 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7496 (mtmt)
REVERT: D  189 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7411 (tttt)
  outliers start: 3
  outliers final: 1
  residues processed: 44
  average time/residue: 1.3200
  time to fit residues: 60.2160
Evaluate side-chains
  45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 LYS
Chi-restraints excluded: chain D residue  210 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.111339 restraints weight = 16809.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.31
r_work: 0.3276 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4612  Z= 0.102
  Angle     :  0.467   4.103   6292  Z= 0.251
  Chirality :  0.039   0.135    716
  Planarity :  0.004   0.046    768
  Dihedral  : 11.943  66.446    800
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 13.22 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.36), residues: 528
  helix:  2.00 (0.33), residues: 248
  sheet: -2.18 (0.46), residues: 84
  loop :  0.06 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 215 
 TYR   0.011   0.001   TYR D 207 
 PHE   0.006   0.001   PHE D 138 
 TRP   0.005   0.001   TRP B 204 
 HIS   0.002   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 4612)
  covalent geometry    : angle       0.46708 ( 6292)
  hydrogen bonds       : bond        0.04287 (  211)
  hydrogen bonds       : angle       3.74189 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2826.87 seconds
wall clock time: 48 minutes 26.68 seconds (2906.68 seconds total)