Starting phenix.real_space_refine
on Fri Sep 11 06:51:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/24vm_69844/09_2026/24vm_69844.cif"
  }
  resolution = 3.54
  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=   0.009 sd=   0.089
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    5373      2.51       5
     N    1299      2.21       5
     O    1362      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8074
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1913
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 5, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1913
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 5, 'TRANS': 233}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 2000
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 4, 'TRANS': 241}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2006
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 4, 'TRANS': 242}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'9PE': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 121
          Unusual residues: {'9PE': 1, 'YJ0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 81
          Unusual residues: {'YJ0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.87, per 1000 atoms: 0.23
  Number of scatterers: 8074
  At special positions: 0
  Unit cell: (82.612, 107.613, 111.961, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       2     15.00
     O    1362      8.00
     N    1299      7.00
     C    5373      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 395.0 milliseconds
  

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      78.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.592A  pdb=" N   ARG A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 142
    Processing helix  chain 'A' and resid 149 through 178
    Processing helix  chain 'A' and resid 196 through 208
      removed outlier: 3.532A  pdb=" N   ALA A 208 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 239
      removed outlier: 3.918A  pdb=" N   GLN A 233 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 257
      removed outlier: 3.895A  pdb=" N   LEU A 249 " --> pdb=" O   GLY A 245 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A 251 " --> pdb=" O   TRP A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 283
    Processing helix  chain 'A' and resid 302 through 315
      removed outlier: 3.505A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 345
      removed outlier: 3.527A  pdb=" N   LEU A 331 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 333 " --> pdb=" O   GLY A 329 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 366
      removed outlier: 3.520A  pdb=" N   LEU A 351 " --> pdb=" O   PRO A 347 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
    Processing helix  chain 'B' and resid 122 through 143
      removed outlier: 4.085A  pdb=" N   HIS B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 178
    Processing helix  chain 'B' and resid 186 through 195
      removed outlier: 4.224A  pdb=" N   LEU B 191 " --> pdb=" O   TRP B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 208
      removed outlier: 3.641A  pdb=" N   ALA B 208 " --> pdb=" O   PHE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 239
    Processing helix  chain 'B' and resid 244 through 257
      removed outlier: 3.601A  pdb=" N   LEU B 249 " --> pdb=" O   GLY B 245 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 283
    Processing helix  chain 'B' and resid 302 through 315
      removed outlier: 3.574A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 345
      removed outlier: 4.118A  pdb=" N   LEU B 331 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ILE B 332 " --> pdb=" O   GLU B 328 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 366
      removed outlier: 3.617A  pdb=" N   LEU B 351 " --> pdb=" O   PRO B 347 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLY B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 85
    Processing helix  chain 'C' and resid 91 through 112
      removed outlier: 4.175A  pdb=" N   HIS C  95 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 147
    Processing helix  chain 'C' and resid 148 through 154
      removed outlier: 5.819A  pdb=" N   CYS C 151 " --> pdb=" O   GLY C 148 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ARG C 152 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR C 153 " --> pdb=" O   CYS C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 163
    Processing helix  chain 'C' and resid 165 through 183
    Processing helix  chain 'C' and resid 201 through 210
      removed outlier: 3.874A  pdb=" N   LEU C 205 " --> pdb=" O   PHE C 201 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   MET C 210 " --> pdb=" O   ARG C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 227
    Processing helix  chain 'C' and resid 229 through 253
    Processing helix  chain 'C' and resid 262 through 275
    Processing helix  chain 'C' and resid 286 through 326
      removed outlier: 4.250A  pdb=" N   LEU C 291 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
      removed outlier: 3.841A  pdb=" N   GLY C 312 " --> pdb=" O   ALA C 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 85
    Processing helix  chain 'D' and resid 93 through 114
      removed outlier: 3.701A  pdb=" N   ILE D 114 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 145
      removed outlier: 3.775A  pdb=" N   SER D 121 " --> pdb=" O   TYR D 117 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TRP D 145 " --> pdb=" O   PHE D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 164
      removed outlier: 3.635A  pdb=" N   ARG D 164 " --> pdb=" O   LEU D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 183
    Processing helix  chain 'D' and resid 200 through 209
      removed outlier: 3.545A  pdb=" N   ILE D 204 " --> pdb=" O   ARG D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 227
    Processing helix  chain 'D' and resid 228 through 253
      removed outlier: 3.696A  pdb=" N   VAL D 232 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 262 through 275
    Processing helix  chain 'D' and resid 286 through 305
      removed outlier: 3.731A  pdb=" N   ALA D 305 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 305 through 326
      removed outlier: 3.513A  pdb=" N   GLY D 312 " --> pdb=" O   ALA D 308 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   SER D 313 " --> pdb=" O   GLY D 309 " (cutoff:3.500A)

    545 hydrogen bonds defined for protein.
    1632 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: 1.18

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1163
        1.31 -     1.43: 2446
        1.43 -     1.56: 4625
        1.56 -     1.68: 6
        1.68 -     1.81: 52
  Bond restraints: 8292
  Sorted by residual:
  bond pdb=" C31 9PE C 902 "
       pdb=" O31 9PE C 902 "
    ideal  model  delta    sigma   weight residual
    1.325  1.399 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C31 9PE B1001 "
       pdb=" O31 9PE B1001 "
    ideal  model  delta    sigma   weight residual
    1.325  1.398 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C21 9PE B1001 "
       pdb=" O21 9PE B1001 "
    ideal  model  delta    sigma   weight residual
    1.329  1.400 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C21 9PE C 902 "
       pdb=" O21 9PE C 902 "
    ideal  model  delta    sigma   weight residual
    1.329  1.399 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CA  ARG D 164 "
       pdb=" CB  ARG D 164 "
    ideal  model  delta    sigma   weight residual
    1.526  1.565 -0.039 1.51e-02 4.39e+03 6.56e+00
  ... (remaining 8287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10925
        2.36 -     4.73: 217
        4.73 -     7.09: 74
        7.09 -     9.45: 21
        9.45 -    11.81: 5
  Bond angle restraints: 11242
  Sorted by residual:
  angle pdb=" CB  LYS D 165 "
        pdb=" CG  LYS D 165 "
        pdb=" CD  LYS D 165 "
      ideal   model   delta    sigma   weight residual
     111.30  122.63  -11.33 2.30e+00 1.89e-01 2.42e+01
  angle pdb=" O12 9PE C 902 "
        pdb=" P   9PE C 902 "
        pdb=" O14 9PE C 902 "
      ideal   model   delta    sigma   weight residual
     120.90  109.09   11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" O12 9PE B1001 "
        pdb=" P   9PE B1001 "
        pdb=" O14 9PE B1001 "
      ideal   model   delta    sigma   weight residual
     120.90  109.28   11.62 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" CA  GLN C  77 "
        pdb=" CB  GLN C  77 "
        pdb=" CG  GLN C  77 "
      ideal   model   delta    sigma   weight residual
     114.10  121.56   -7.46 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" O11 9PE C 902 "
        pdb=" P   9PE C 902 "
        pdb=" O13 9PE C 902 "
      ideal   model   delta    sigma   weight residual
      99.99  110.56  -10.57 3.00e+00 1.11e-01 1.24e+01
  ... (remaining 11237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 4680
       35.92 -    71.85: 279
       71.85 -   107.77: 48
      107.77 -   143.70: 51
      143.70 -   179.62: 18
  Dihedral angle restraints: 5076
    sinusoidal: 2283
      harmonic: 2793
  Sorted by residual:
  dihedral pdb=" O30 YJ0 D 901 "
           pdb=" C31 YJ0 D 901 "
           pdb=" C32 YJ0 D 901 "
           pdb=" O52 YJ0 D 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -125.08   54.54 -179.62     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" N   9PE C 902 "
           pdb=" C11 9PE C 902 "
           pdb=" C12 9PE C 902 "
           pdb=" O13 9PE C 902 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.84  111.31 -178.15     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O21 9PE B1001 "
           pdb=" C2  9PE B1001 "
           pdb=" C3  9PE B1001 "
           pdb=" O31 9PE B1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.43  120.13 -176.56     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 5073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.216: 1264
       1.216 -    2.432: 0
       2.432 -    3.648: 0
       3.648 -    4.864: 1
       4.864 -    6.080: 18
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" C12 YJ0 D 901 "
            pdb=" C11 YJ0 D 901 "
            pdb=" C13 YJ0 D 901 "
            pdb=" C7  YJ0 D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      3.10   -2.98    6.08 2.00e-01 2.50e+01 9.24e+02
  chirality pdb=" C12 YJ0 C 901 "
            pdb=" C11 YJ0 C 901 "
            pdb=" C13 YJ0 C 901 "
            pdb=" C7  YJ0 C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      3.10   -2.95    6.05 2.00e-01 2.50e+01 9.15e+02
  chirality pdb=" C16 YJ0 D 901 "
            pdb=" C11 YJ0 D 901 "
            pdb=" C15 YJ0 D 901 "
            pdb=" C17 YJ0 D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.82    2.73   -5.55 2.00e-01 2.50e+01 7.70e+02
  ... (remaining 1280 not shown)

  Planarity restraints: 1317
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 YJ0 C 901 "   -0.215 2.00e-02 2.50e+03   1.79e-01 4.01e+02
        pdb=" C18 YJ0 C 901 "    0.268 2.00e-02 2.50e+03
        pdb=" C19 YJ0 C 901 "    0.110 2.00e-02 2.50e+03
        pdb=" C20 YJ0 C 901 "    0.011 2.00e-02 2.50e+03
        pdb=" C24 YJ0 C 901 "   -0.174 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 YJ0 D 901 "    0.120 2.00e-02 2.50e+03   1.00e-01 1.25e+02
        pdb=" C18 YJ0 D 901 "   -0.150 2.00e-02 2.50e+03
        pdb=" C19 YJ0 D 901 "   -0.057 2.00e-02 2.50e+03
        pdb=" C20 YJ0 D 901 "   -0.012 2.00e-02 2.50e+03
        pdb=" C24 YJ0 D 901 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 176 "   -0.009 2.00e-02 2.50e+03   1.30e-02 4.25e+00
        pdb=" CG  TRP B 176 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 176 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 176 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 176 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 176 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1314 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1691
        2.78 -     3.31: 7886
        3.31 -     3.84: 13289
        3.84 -     4.37: 14039
        4.37 -     4.90: 25049
  Nonbonded interactions: 61954
  Sorted by model distance:
  nonbonded pdb=" O   LEU D 271 "
            pdb=" OG1 THR D 275 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR A 313 "
            pdb=" OH  TYR B 319 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR A 319 "
            pdb=" OG1 THR D 273 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OE1 GLU C  85 "
            pdb=" O51 YJ0 C 901 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER C 109 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.282 3.040
  ... (remaining 61949 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' and resid 110 through 366)
}
ncs_group {
  reference = (chain 'C' and resid 70 through 901)
  selection = (chain 'D' and (resid 70 through 183 or resid 195 through 901))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.490
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
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      :  0.005   0.074   8292  Z= 0.228
  Angle     :  0.944  11.814  11242  Z= 0.447
  Chirality :  0.643   6.080   1283
  Planarity :  0.007   0.179   1317
  Dihedral  : 29.616 179.621   3290
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.49 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 31.01 %
    Favored  : 68.49 %
  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 (0.28), residues: 955
  helix:  1.36 (0.20), residues: 738
  sheet:  None (None), residues: 0
  loop : -3.42 (0.37), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 195 
 TYR   0.017   0.001   TYR C 153 
 PHE   0.019   0.002   PHE B 167 
 TRP   0.034   0.002   TRP B 176 
 HIS   0.001   0.000   HIS D 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.23 ( 8292)
  covalent geometry    : angle       0.94447 /  0.45 (11242)
  hydrogen bonds       : bond        0.13367 /  8.18 (  545)
  hydrogen bonds       : angle       5.36230 /  3.87 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 178
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 GLU cc_start: 0.7893 (tp30) cc_final: 0.6965 (tt0)
REVERT: C  141 PHE cc_start: 0.8120 (m-80) cc_final: 0.7500 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 178
  average time/residue: 0.1023
  time to fit residues: 24.2761
Evaluate side-chains
  170 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 167
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  207 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 GLN
C 320 GLN
C 323 HIS
D 285 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.187747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.142958 restraints weight = 12573.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.146374 restraints weight = 7103.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.148121 restraints weight = 5178.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.149518 restraints weight = 4397.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.149727 restraints weight = 4019.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8292  Z= 0.154
  Angle     :  1.160  35.931  11242  Z= 0.455
  Chirality :  0.117   2.211   1283
  Planarity :  0.004   0.042   1317
  Dihedral  : 24.612 178.475   1549
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.70 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 26.90 %
    Favored  : 69.24 %
  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:  0.70 (0.28), residues: 955
  helix:  1.57 (0.20), residues: 743
  sheet:  None (None), residues: 0
  loop : -3.74 (0.34), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 154 
 TYR   0.012   0.001   TYR C 153 
 PHE   0.026   0.001   PHE D  99 
 TRP   0.013   0.001   TRP B 176 
 HIS   0.006   0.001   HIS C 323 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 8292)
  covalent geometry    : angle       1.16049 /  0.46 (11242)
  hydrogen bonds       : bond        0.05328 /  3.50 (  545)
  hydrogen bonds       : angle       4.45411 /  3.22 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 LYS cc_start: 0.7207 (mptt) cc_final: 0.6570 (mmtm)
REVERT: A  361 GLU cc_start: 0.7760 (tp30) cc_final: 0.6875 (tt0)
REVERT: B  237 MET cc_start: 0.8456 (mmm) cc_final: 0.8203 (mmm)
REVERT: B  265 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.6486 (m-10)
REVERT: C   77 GLN cc_start: 0.8578 (pp30) cc_final: 0.8344 (pp30)
REVERT: C  141 PHE cc_start: 0.8268 (m-80) cc_final: 0.7733 (m-80)
REVERT: C  220 LEU cc_start: 0.9165 (tt) cc_final: 0.8857 (tp)
  outliers start: 31
  outliers final: 16
  residues processed: 191
  average time/residue: 0.0989
  time to fit residues: 25.1288
Evaluate side-chains
  177 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  322 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 320 GLN
D  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.169520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.130765 restraints weight = 11897.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129567 restraints weight = 9867.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130391 restraints weight = 9384.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131139 restraints weight = 8280.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131146 restraints weight = 6910.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8292  Z= 0.237
  Angle     :  1.185  34.723  11242  Z= 0.478
  Chirality :  0.115   2.194   1283
  Planarity :  0.004   0.038   1317
  Dihedral  : 23.642 179.513   1543
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.81 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 26.90 %
    Favored  : 68.24 %
  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:  0.66 (0.28), residues: 955
  helix:  1.50 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -3.51 (0.37), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 212 
 TYR   0.024   0.002   TYR A 184 
 PHE   0.017   0.002   PHE B 269 
 TRP   0.014   0.002   TRP A 308 
 HIS   0.003   0.001   HIS A 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.24 ( 8292)
  covalent geometry    : angle       1.18509 /  0.48 (11242)
  hydrogen bonds       : bond        0.06239 /  4.15 (  545)
  hydrogen bonds       : angle       4.59974 /  3.34 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.6270 (m-80)
REVERT: A  184 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5787 (m-10)
REVERT: A  196 LYS cc_start: 0.7460 (mptt) cc_final: 0.7073 (mmtm)
REVERT: A  199 CYS cc_start: 0.8188 (t) cc_final: 0.7948 (t)
REVERT: B  265 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.6635 (m-10)
REVERT: C  141 PHE cc_start: 0.8148 (m-80) cc_final: 0.7510 (m-80)
REVERT: C  171 ASP cc_start: 0.7164 (m-30) cc_final: 0.6884 (m-30)
REVERT: D  152 ARG cc_start: 0.6242 (tmm-80) cc_final: 0.5900 (tmm-80)
REVERT: D  258 ASP cc_start: 0.8483 (t0) cc_final: 0.8026 (t0)
  outliers start: 39
  outliers final: 23
  residues processed: 181
  average time/residue: 0.0889
  time to fit residues: 21.6074
Evaluate side-chains
  173 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 TYR
Chi-restraints excluded: chain A residue  184 TYR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  283 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  178 SER
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  322 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0070
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.6598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
C 320 GLN
C 323 HIS
D  77 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.182868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139774 restraints weight = 12305.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.143149 restraints weight = 6891.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.145258 restraints weight = 4972.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146495 restraints weight = 4178.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.146942 restraints weight = 3819.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8292  Z= 0.142
  Angle     :  1.125  34.714  11242  Z= 0.439
  Chirality :  0.112   2.136   1283
  Planarity :  0.004   0.042   1317
  Dihedral  : 22.943 177.263   1543
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.49 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 29.89 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.98 (0.28), residues: 955
  helix:  1.74 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop : -3.43 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 239 
 TYR   0.019   0.001   TYR A 184 
 PHE   0.015   0.001   PHE D  99 
 TRP   0.015   0.001   TRP C 145 
 HIS   0.007   0.001   HIS C 323 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.14 ( 8292)
  covalent geometry    : angle       1.12457 /  0.44 (11242)
  hydrogen bonds       : bond        0.04977 /  3.27 (  545)
  hydrogen bonds       : angle       4.30591 /  3.10 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 LYS cc_start: 0.7457 (mptt) cc_final: 0.7128 (mmtm)
REVERT: A  199 CYS cc_start: 0.8283 (t) cc_final: 0.8015 (t)
REVERT: B  265 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.6579 (m-10)
REVERT: C  116 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6674 (pm20)
REVERT: C  141 PHE cc_start: 0.8177 (m-80) cc_final: 0.7697 (m-80)
REVERT: C  171 ASP cc_start: 0.7472 (m-30) cc_final: 0.6901 (m-30)
REVERT: D  152 ARG cc_start: 0.5968 (tmm-80) cc_final: 0.5667 (tmm-80)
REVERT: D  203 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7495 (mt0)
REVERT: D  258 ASP cc_start: 0.8406 (t0) cc_final: 0.7961 (t0)
  outliers start: 29
  outliers final: 17
  residues processed: 183
  average time/residue: 0.0973
  time to fit residues: 23.8125
Evaluate side-chains
  171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  283 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  178 SER
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0040
   chunk 80 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
C 320 GLN
D  77 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.168048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.129833 restraints weight = 11979.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.128599 restraints weight = 9610.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129152 restraints weight = 8390.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129470 restraints weight = 7471.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129778 restraints weight = 6825.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8292  Z= 0.139
  Angle     :  1.123  34.662  11242  Z= 0.438
  Chirality :  0.112   2.120   1283
  Planarity :  0.004   0.045   1317
  Dihedral  : 22.614 178.459   1543
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.28 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.27 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.29), residues: 955
  helix:  1.80 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop : -3.35 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 143 
 TYR   0.015   0.001   TYR A 184 
 PHE   0.014   0.001   PHE A 162 
 TRP   0.017   0.001   TRP B 327 
 HIS   0.002   0.000   HIS B 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.14 ( 8292)
  covalent geometry    : angle       1.12347 /  0.44 (11242)
  hydrogen bonds       : bond        0.04907 /  3.25 (  545)
  hydrogen bonds       : angle       4.23446 /  3.04 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 162
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 CYS cc_start: 0.8286 (t) cc_final: 0.8081 (t)
REVERT: B  131 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7843 (tp)
REVERT: B  265 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.6680 (m-10)
REVERT: B  288 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5693 (tt0)
REVERT: B  295 GLU cc_start: 0.4362 (OUTLIER) cc_final: 0.3868 (pm20)
REVERT: D  152 ARG cc_start: 0.6005 (tmm-80) cc_final: 0.5690 (tmm-80)
REVERT: D  203 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7476 (mt0)
REVERT: D  258 ASP cc_start: 0.8358 (t0) cc_final: 0.7897 (t0)
  outliers start: 39
  outliers final: 29
  residues processed: 187
  average time/residue: 0.0958
  time to fit residues: 24.0684
Evaluate side-chains
  186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  283 GLU
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  178 SER
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  322 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
C 320 GLN
C 323 HIS
D  77 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.167897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.128647 restraints weight = 11853.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129343 restraints weight = 8324.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.129576 restraints weight = 7144.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129566 restraints weight = 6464.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.129839 restraints weight = 6342.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8292  Z= 0.148
  Angle     :  1.139  34.610  11242  Z= 0.447
  Chirality :  0.112   2.100   1283
  Planarity :  0.004   0.045   1317
  Dihedral  : 22.392 178.816   1543
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.18 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 27.90 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.29), residues: 955
  helix:  1.89 (0.19), residues: 737
  sheet:  None (None), residues: 0
  loop : -3.24 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 206 
 TYR   0.014   0.001   TYR A 184 
 PHE   0.018   0.001   PHE A 167 
 TRP   0.018   0.001   TRP B 327 
 HIS   0.007   0.001   HIS C 323 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 ( 8292)
  covalent geometry    : angle       1.13857 /  0.45 (11242)
  hydrogen bonds       : bond        0.04956 /  3.29 (  545)
  hydrogen bonds       : angle       4.22128 /  3.02 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 159
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  131 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7872 (tp)
REVERT: B  200 MET cc_start: 0.6655 (ttt) cc_final: 0.6277 (tpp)
REVERT: B  265 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.6681 (m-10)
REVERT: B  288 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5694 (tt0)
REVERT: B  295 GLU cc_start: 0.4394 (OUTLIER) cc_final: 0.3809 (pm20)
REVERT: C  165 LYS cc_start: 0.8101 (tppt) cc_final: 0.7892 (mttp)
REVERT: D  203 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7623 (mt0)
REVERT: D  258 ASP cc_start: 0.8396 (t0) cc_final: 0.7939 (t0)
  outliers start: 39
  outliers final: 28
  residues processed: 186
  average time/residue: 0.0998
  time to fit residues: 24.8448
Evaluate side-chains
  186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 153
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  284 LYS
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  162 PHE
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  178 SER
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  288 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
C 320 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.167470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.130255 restraints weight = 12039.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.129174 restraints weight = 10561.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130638 restraints weight = 9618.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130785 restraints weight = 8086.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131399 restraints weight = 7261.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8292  Z= 0.155
  Angle     :  1.143  34.661  11242  Z= 0.452
  Chirality :  0.112   2.089   1283
  Planarity :  0.004   0.042   1317
  Dihedral  : 22.355 179.272   1543
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.28 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 29.02 %
    Favored  : 66.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.29), residues: 955
  helix:  1.86 (0.19), residues: 745
  sheet:  None (None), residues: 0
  loop : -3.58 (0.37), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 119 
 TYR   0.011   0.001   TYR A 184 
 PHE   0.013   0.001   PHE A 162 
 TRP   0.019   0.001   TRP A 327 
 HIS   0.002   0.000   HIS A 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 8292)
  covalent geometry    : angle       1.14337 /  0.45 (11242)
  hydrogen bonds       : bond        0.04996 /  3.32 (  545)
  hydrogen bonds       : angle       4.20979 /  3.01 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  131 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7953 (tp)
REVERT: B  265 TRP cc_start: 0.7827 (OUTLIER) cc_final: 0.6692 (m-10)
REVERT: B  288 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5851 (tt0)
REVERT: B  295 GLU cc_start: 0.4268 (OUTLIER) cc_final: 0.3474 (pm20)
REVERT: B  296 MET cc_start: 0.6999 (ppp) cc_final: 0.6308 (ppp)
REVERT: D  258 ASP cc_start: 0.8394 (t0) cc_final: 0.7940 (t0)
  outliers start: 37
  outliers final: 27
  residues processed: 182
  average time/residue: 0.0935
  time to fit residues: 22.9777
Evaluate side-chains
  180 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  178 SER
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  288 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
C 320 GLN
D  77 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.165201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.126875 restraints weight = 12058.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128407 restraints weight = 10759.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.128773 restraints weight = 8899.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.128982 restraints weight = 7411.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.129071 restraints weight = 6671.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8292  Z= 0.191
  Angle     :  1.172  34.532  11242  Z= 0.469
  Chirality :  0.112   2.074   1283
  Planarity :  0.004   0.041   1317
  Dihedral  : 22.276 179.775   1541
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.81 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.27 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.29), residues: 955
  helix:  1.85 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop : -3.35 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 152 
 TYR   0.017   0.001   TYR D 153 
 PHE   0.027   0.001   PHE A 171 
 TRP   0.022   0.002   TRP A 327 
 HIS   0.002   0.001   HIS A 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.19 ( 8292)
  covalent geometry    : angle       1.17185 /  0.47 (11242)
  hydrogen bonds       : bond        0.05465 /  3.64 (  545)
  hydrogen bonds       : angle       4.30151 /  3.08 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  265 TRP cc_start: 0.7816 (OUTLIER) cc_final: 0.6676 (m-10)
REVERT: B  288 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5887 (tt0)
REVERT: C  288 ASN cc_start: 0.7213 (m-40) cc_final: 0.6879 (p0)
REVERT: D  258 ASP cc_start: 0.8444 (t0) cc_final: 0.7920 (t0)
  outliers start: 39
  outliers final: 29
  residues processed: 183
  average time/residue: 0.1012
  time to fit residues: 24.6846
Evaluate side-chains
  184 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  207 MET
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  288 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 83 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 362 GLN
B 233 GLN
C 320 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.168244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.128655 restraints weight = 12086.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.128364 restraints weight = 10122.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129161 restraints weight = 7602.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.129526 restraints weight = 6838.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129753 restraints weight = 6269.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8292  Z= 0.142
  Angle     :  1.152  34.217  11242  Z= 0.456
  Chirality :  0.112   2.085   1283
  Planarity :  0.004   0.053   1317
  Dihedral  : 22.109 179.724   1541
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.39 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 30.51 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 955
  helix:  1.94 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop : -3.37 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 152 
 TYR   0.011   0.001   TYR A 184 
 PHE   0.013   0.001   PHE A 171 
 TRP   0.024   0.002   TRP A 327 
 HIS   0.002   0.000   HIS D 259 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 8292)
  covalent geometry    : angle       1.15200 /  0.46 (11242)
  hydrogen bonds       : bond        0.04804 /  3.18 (  545)
  hydrogen bonds       : angle       4.19676 /  2.99 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 GLU cc_start: 0.8096 (tp30) cc_final: 0.7000 (tt0)
REVERT: B  265 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.6696 (m-10)
REVERT: B  288 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5764 (tt0)
REVERT: B  296 MET cc_start: 0.6981 (ppp) cc_final: 0.6515 (ppp)
REVERT: C   77 GLN cc_start: 0.8565 (pp30) cc_final: 0.8344 (pp30)
REVERT: D  258 ASP cc_start: 0.8441 (t0) cc_final: 0.7991 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 178
  average time/residue: 0.0977
  time to fit residues: 23.4780
Evaluate side-chains
  171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue  184 TYR
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  286 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 320 GLN
D  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.167657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.128249 restraints weight = 12026.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.127831 restraints weight = 8923.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128599 restraints weight = 7486.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.128904 restraints weight = 6487.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.129167 restraints weight = 6063.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8292  Z= 0.149
  Angle     :  1.157  34.266  11242  Z= 0.460
  Chirality :  0.112   2.068   1283
  Planarity :  0.005   0.093   1317
  Dihedral  : 22.088 179.780   1541
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.60 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 30.26 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.28), residues: 955
  helix:  1.90 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -3.53 (0.37), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 239 
 TYR   0.011   0.001   TYR D  73 
 PHE   0.014   0.001   PHE A 162 
 TRP   0.032   0.002   TRP D 145 
 HIS   0.002   0.000   HIS B 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 ( 8292)
  covalent geometry    : angle       1.15724 /  0.46 (11242)
  hydrogen bonds       : bond        0.04916 /  3.26 (  545)
  hydrogen bonds       : angle       4.18845 /  2.99 ( 1632)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  265 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.6716 (m-10)
REVERT: B  288 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5806 (tt0)
REVERT: B  296 MET cc_start: 0.7031 (ppp) cc_final: 0.6225 (ppp)
REVERT: C   77 GLN cc_start: 0.8635 (pp30) cc_final: 0.8398 (pp30)
REVERT: C  165 LYS cc_start: 0.8032 (tppt) cc_final: 0.7721 (mttp)
REVERT: D  258 ASP cc_start: 0.8408 (t0) cc_final: 0.7958 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 172
  average time/residue: 0.0993
  time to fit residues: 22.8891
Evaluate side-chains
  167 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue  265 TRP
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  275 THR
Chi-restraints excluded: chain C residue  297 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  275 THR
Chi-restraints excluded: chain D residue  286 THR
Chi-restraints excluded: chain D residue  288 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.167579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.127124 restraints weight = 12068.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.127911 restraints weight = 7915.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.128564 restraints weight = 6424.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129235 restraints weight = 5740.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129258 restraints weight = 5558.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8292  Z= 0.150
  Angle     :  1.170  34.242  11242  Z= 0.468
  Chirality :  0.112   2.063   1283
  Planarity :  0.004   0.041   1317
  Dihedral  : 21.967 179.677   1541
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.70 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 30.76 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.28), residues: 955
  helix:  1.91 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -3.35 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 152 
 TYR   0.009   0.001   TYR A 184 
 PHE   0.014   0.001   PHE A 162 
 TRP   0.028   0.002   TRP D 145 
 HIS   0.002   0.000   HIS B 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 8292)
  covalent geometry    : angle       1.17007 /  0.47 (11242)
  hydrogen bonds       : bond        0.04896 /  3.25 (  545)
  hydrogen bonds       : angle       4.20335 /  3.00 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1455.55 seconds
wall clock time: 25 minutes 49.92 seconds (1549.92 seconds total)