Starting phenix.real_space_refine
on Wed Aug  5 00:10:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n9c_49165/08_2026/9n9c_49165.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    4520      2.51       5
     N    1353      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2860
          Classifications: {'peptide': 346}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 338}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2860
          Classifications: {'peptide': 346}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 338}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 1881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 1881
          Classifications: {'RNA': 88}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 9, 'rna3p': 78}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.18, per 1000 atoms: 0.16
  Number of scatterers: 7602
  At special positions: 0
  Unit cell: (84.666, 107.682, 100.284, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P      88     15.00
     Mg      1     11.99
     O    1610      8.00
     N    1353      7.00
     C    4520      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: 0.45
  Conformation dependent library (CDL) restraints added in 191.7 milliseconds
  

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1308

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 6 sheets defined
      48.0% alpha, 25.0% beta
      25 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 63
      removed outlier: 3.835A  pdb=" N   LYS A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 96
    Processing helix  chain 'A' and resid 102 through 119
    Processing helix  chain 'A' and resid 119 through 126
    Processing helix  chain 'A' and resid 177 through 188
      removed outlier: 3.677A  pdb=" N   LYS A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 270
      removed outlier: 4.308A  pdb=" N   TYR A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ARG A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 4.246A  pdb=" N   ARG A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 315
      removed outlier: 4.236A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 359
      removed outlier: 3.900A  pdb=" N   TYR A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA A 358 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 54
    Processing helix  chain 'B' and resid 84 through 96
      removed outlier: 4.207A  pdb=" N   THR B  88 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 126
      removed outlier: 3.612A  pdb=" N   LEU B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   VAL B 121 " --> pdb=" O   ASN B 117 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   GLN B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 188
    Processing helix  chain 'B' and resid 248 through 272
      removed outlier: 4.713A  pdb=" N   ARG B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ARG B 256 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 315
      removed outlier: 5.396A  pdb=" N   ALA B 285 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   VAL B 286 " --> pdb=" O   LYS B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 359
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141
      removed outlier: 4.137A  pdb=" N   ILE A 204 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   PHE A 158 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA A 157 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   TYR A 151 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   CYS A 159 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A 149 " --> pdb=" O   CYS A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141
      removed outlier: 4.636A  pdb=" N   LYS A 191 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246
      removed outlier: 3.604A  pdb=" N   ILE A 235 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   ALA A 317 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL A 223 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   THR A 319 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 225 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 321 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   MET A 323 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141
      removed outlier: 3.732A  pdb=" N   SER B 195 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE B 204 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   PHE B 158 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA B 157 " --> pdb=" O   TYR B 151 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   TYR B 151 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   CYS B 159 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LEU B 149 " --> pdb=" O   CYS B 159 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 141
      removed outlier: 3.732A  pdb=" N   SER B 195 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246
      removed outlier: 3.755A  pdb=" N   ILE B 235 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   ALA B 317 " --> pdb=" O   PRO B 221 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY B 318 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ILE B 363 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 320 " --> pdb=" O   ILE B 363 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   GLY B 365 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU B 322 " --> pdb=" O   GLY B 365 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    1014 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      62 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1801
        1.33 -     1.45: 2023
        1.45 -     1.57: 3884
        1.57 -     1.69: 175
        1.69 -     1.81: 52
  Bond restraints: 7935
  Sorted by residual:
  bond pdb=" N7    G c  29 "
       pdb=" C5    G c  29 "
    ideal  model  delta    sigma   weight residual
    1.388  1.373  0.015 6.00e-03 2.78e+04 6.41e+00
  bond pdb=" N9    A c  46 "
       pdb=" C4    A c  46 "
    ideal  model  delta    sigma   weight residual
    1.374  1.359  0.015 6.00e-03 2.78e+04 6.24e+00
  bond pdb=" C5    G c  27 "
       pdb=" C4    G c  27 "
    ideal  model  delta    sigma   weight residual
    1.379  1.363  0.016 7.00e-03 2.04e+04 5.37e+00
  bond pdb=" C5    G c   6 "
       pdb=" C4    G c   6 "
    ideal  model  delta    sigma   weight residual
    1.379  1.363  0.016 7.00e-03 2.04e+04 4.99e+00
  bond pdb=" N3    C c  13 "
       pdb=" C4    C c  13 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 7.00e-03 2.04e+04 4.18e+00
  ... (remaining 7930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 10947
        2.68 -     5.36: 124
        5.36 -     8.03: 8
        8.03 -    10.71: 1
       10.71 -    13.39: 1
  Bond angle restraints: 11081
  Sorted by residual:
  angle pdb=" O4'   G c  28 "
        pdb=" C1'   G c  28 "
        pdb=" N9    G c  28 "
      ideal   model   delta    sigma   weight residual
     108.20  112.32   -4.12 8.00e-01 1.56e+00 2.66e+01
  angle pdb=" C1'   U c  30 "
        pdb=" N1    U c  30 "
        pdb=" C2    U c  30 "
      ideal   model   delta    sigma   weight residual
     117.70  122.77   -5.07 1.20e+00 6.94e-01 1.78e+01
  angle pdb=" O5'   G c  29 "
        pdb=" C5'   G c  29 "
        pdb=" C4'   G c  29 "
      ideal   model   delta    sigma   weight residual
     109.40  112.78   -3.38 8.00e-01 1.56e+00 1.78e+01
  angle pdb=" O5'   A c  50 "
        pdb=" C5'   A c  50 "
        pdb=" C4'   A c  50 "
      ideal   model   delta    sigma   weight residual
     109.40  112.75   -3.35 8.00e-01 1.56e+00 1.75e+01
  angle pdb=" C1'   C c  13 "
        pdb=" N1    C c  13 "
        pdb=" C2    C c  13 "
      ideal   model   delta    sigma   weight residual
     118.80  123.35   -4.55 1.10e+00 8.26e-01 1.71e+01
  ... (remaining 11076 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.72: 4507
       32.72 -    65.45: 362
       65.45 -    98.17: 28
       98.17 -   130.89: 0
      130.89 -   163.62: 1
  Dihedral angle restraints: 4898
    sinusoidal: 2869
      harmonic: 2029
  Sorted by residual:
  dihedral pdb=" O4'   C c  13 "
           pdb=" C1'   C c  13 "
           pdb=" N1    C c  13 "
           pdb=" C2    C c  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.38  163.62     1      1.50e+01 4.44e-03 8.36e+01
  dihedral pdb=" CA  MET B  85 "
           pdb=" C   MET B  85 "
           pdb=" N   ASN B  86 "
           pdb=" CA  ASN B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  TYR A 272 "
           pdb=" C   TYR A 272 "
           pdb=" N   SER A 273 "
           pdb=" CA  SER A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 4895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 784
       0.036 -    0.072: 306
       0.072 -    0.108: 83
       0.108 -    0.144: 108
       0.144 -    0.180: 3
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" C2'   G c  28 "
            pdb=" C3'   G c  28 "
            pdb=" O2'   G c  28 "
            pdb=" C1'   G c  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.60   -2.42   -0.18 2.00e-01 2.50e+01 8.09e-01
  chirality pdb=" CB  THR B 292 "
            pdb=" CA  THR B 292 "
            pdb=" OG1 THR B 292 "
            pdb=" CG2 THR B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CB  ILE B  14 "
            pdb=" CA  ILE B  14 "
            pdb=" CG1 ILE B  14 "
            pdb=" CG2 ILE B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 1281 not shown)

  Planarity restraints: 1057
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G c  28 "   -0.061 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        pdb=" N9    G c  28 "    0.064 2.00e-02 2.50e+03
        pdb=" C8    G c  28 "    0.008 2.00e-02 2.50e+03
        pdb=" N7    G c  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G c  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G c  28 "   -0.014 2.00e-02 2.50e+03
        pdb=" O6    G c  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G c  28 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G c  28 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G c  28 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G c  28 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G c  28 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 184 "    0.255 9.50e-02 1.11e+02   1.15e-01 8.37e+00
        pdb=" NE  ARG B 184 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 184 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 184 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 184 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A c  53 "   -0.024 2.00e-02 2.50e+03   1.20e-02 3.95e+00
        pdb=" N9    A c  53 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A c  53 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A c  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A c  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A c  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A c  53 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A c  53 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A c  53 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A c  53 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A c  53 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1054 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 109
        2.64 -     3.20: 6572
        3.20 -     3.77: 12627
        3.77 -     4.33: 16647
        4.33 -     4.90: 25229
  Nonbonded interactions: 61184
  Sorted by model distance:
  nonbonded pdb=" N2    G c  16 "
            pdb=" O2    C c  71 "
     model   vdw
     2.073 2.496
  nonbonded pdb=" NH1 ARG A  10 "
            pdb=" OP2   U c  75 "
     model   vdw
     2.136 3.120
  nonbonded pdb=" O   GLU A 251 "
            pdb=" OH  TYR A 296 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" ND2 ASN A  43 "
            pdb=" O   GLU B 127 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O2'   C c  23 "
            pdb=" N3    A c  53 "
     model   vdw
     2.248 3.120
  ... (remaining 61179 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.660
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
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   0.057   7935  Z= 0.317
  Angle     :  0.723  13.388  11081  Z= 0.498
  Chirality :  0.052   0.180   1284
  Planarity :  0.005   0.115   1057
  Dihedral  : 19.867 163.616   3590
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.43 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.51 %
    Favored  : 68.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.32), residues: 682
  helix:  1.29 (0.29), residues: 319
  sheet: -0.66 (0.50), residues: 113
  loop : -2.25 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 184 
 TYR   0.012   0.001   TYR B 254 
 PHE   0.021   0.002   PHE A  39 
 TRP   0.026   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B 302 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.32 ( 7935)
  covalent geometry    : angle       0.72263 /  0.50 (11081)
  hydrogen bonds       : bond        0.13996 /  8.97 (  396)
  hydrogen bonds       : angle       5.71326 /  4.24 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.7458 (m-30) cc_final: 0.7165 (m-30)
REVERT: A   53 GLU cc_start: 0.7394 (tt0) cc_final: 0.5945 (tt0)
REVERT: A  130 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6566 (mp)
REVERT: A  134 LYS cc_start: 0.7435 (mmtt) cc_final: 0.7191 (mmtt)
REVERT: A  174 ASP cc_start: 0.7733 (t0) cc_final: 0.7271 (t0)
REVERT: A  184 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7229 (mtp85)
REVERT: A  263 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7542 (ttm170)
REVERT: A  280 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7453 (mttt)
REVERT: B   57 ASP cc_start: 0.6885 (m-30) cc_final: 0.6617 (m-30)
REVERT: B   91 VAL cc_start: 0.7885 (t) cc_final: 0.7640 (p)
REVERT: B  100 MET cc_start: 0.4754 (tpt) cc_final: 0.3979 (tpt)
REVERT: B  139 PHE cc_start: 0.7723 (p90) cc_final: 0.7273 (p90)
REVERT: B  223 VAL cc_start: 0.8678 (p) cc_final: 0.8352 (m)
REVERT: B  231 LEU cc_start: 0.8798 (mt) cc_final: 0.8591 (mt)
REVERT: B  232 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6953 (mm-30)
REVERT: B  241 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7703 (tmtt)
REVERT: B  342 TRP cc_start: 0.8414 (m100) cc_final: 0.8154 (m100)
  outliers start: 24
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0945
  time to fit residues: 17.4694
Evaluate side-chains
  158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  293 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   85 MET
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 ARG
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  52 GLN
A 315 HIS
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.184751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.152464 restraints weight = 11055.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.32
r_work: 0.3754 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.0692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7935  Z= 0.153
  Angle     :  0.541  11.500  11081  Z= 0.296
  Chirality :  0.040   0.299   1284
  Planarity :  0.004   0.041   1057
  Dihedral  : 19.081 161.381   2157
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.69 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 24.43 %
    Favored  : 69.58 %
  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: -0.09 (0.32), residues: 682
  helix:  1.70 (0.28), residues: 317
  sheet: -0.84 (0.47), residues: 124
  loop : -2.07 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 184 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.018   0.002   PHE A  39 
 TRP   0.008   0.001   TRP B 342 
 HIS   0.005   0.001   HIS A 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 7935)
  covalent geometry    : angle       0.54088 /  0.30 (11081)
  hydrogen bonds       : bond        0.05819 /  4.02 (  396)
  hydrogen bonds       : angle       4.57107 /  3.36 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7379 (tt0) cc_final: 0.5868 (tt0)
REVERT: A  134 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7164 (mmtt)
REVERT: A  180 MET cc_start: 0.6915 (mmt) cc_final: 0.6612 (mmt)
REVERT: A  184 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7474 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8150 (ptpt)
REVERT: A  263 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7545 (ttm170)
REVERT: A  280 LYS cc_start: 0.7941 (tttt) cc_final: 0.7651 (mttt)
REVERT: B   57 ASP cc_start: 0.6862 (m-30) cc_final: 0.6574 (m-30)
REVERT: B   91 VAL cc_start: 0.7903 (t) cc_final: 0.7663 (p)
REVERT: B  139 PHE cc_start: 0.7725 (p90) cc_final: 0.7227 (p90)
REVERT: B  146 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5806 (tt)
REVERT: B  191 LYS cc_start: 0.7155 (tttt) cc_final: 0.6909 (tttm)
REVERT: B  231 LEU cc_start: 0.8751 (mt) cc_final: 0.8550 (tp)
REVERT: B  232 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6883 (mm-30)
REVERT: B  241 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7661 (tmtt)
REVERT: B  342 TRP cc_start: 0.8486 (m100) cc_final: 0.8127 (m100)
  outliers start: 37
  outliers final: 20
  residues processed: 151
  average time/residue: 0.0980
  time to fit residues: 18.5917
Evaluate side-chains
  150 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  125 LYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  128 ARG
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  303 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0670
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.8122

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.185118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.152726 restraints weight = 10977.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.32
r_work: 0.3755 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7935  Z= 0.145
  Angle     :  0.511  11.325  11081  Z= 0.279
  Chirality :  0.039   0.307   1284
  Planarity :  0.004   0.039   1057
  Dihedral  : 18.856 161.214   2130
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.55 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 25.24 %
    Favored  : 68.28 %
  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:  0.06 (0.32), residues: 682
  helix:  1.81 (0.27), residues: 317
  sheet: -0.86 (0.47), residues: 126
  loop : -1.93 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 184 
 TYR   0.014   0.001   TYR B 353 
 PHE   0.016   0.002   PHE A  39 
 TRP   0.005   0.001   TRP A 124 
 HIS   0.005   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.15 ( 7935)
  covalent geometry    : angle       0.51115 /  0.28 (11081)
  hydrogen bonds       : bond        0.05455 /  3.76 (  396)
  hydrogen bonds       : angle       4.33543 /  3.19 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7369 (tt0) cc_final: 0.5837 (tt0)
REVERT: A  134 LYS cc_start: 0.7421 (mmtt) cc_final: 0.7173 (mmtt)
REVERT: A  180 MET cc_start: 0.6937 (mmt) cc_final: 0.6688 (mmt)
REVERT: A  184 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7417 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8129 (ptpt)
REVERT: A  263 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7528 (ttm170)
REVERT: B   57 ASP cc_start: 0.6868 (m-30) cc_final: 0.6594 (m-30)
REVERT: B   91 VAL cc_start: 0.7896 (t) cc_final: 0.7659 (p)
REVERT: B  139 PHE cc_start: 0.7696 (p90) cc_final: 0.7191 (p90)
REVERT: B  191 LYS cc_start: 0.7112 (tttt) cc_final: 0.6877 (tttm)
REVERT: B  232 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6871 (mm-30)
REVERT: B  241 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7667 (tmtt)
REVERT: B  342 TRP cc_start: 0.8484 (m100) cc_final: 0.8278 (m100)
  outliers start: 40
  outliers final: 28
  residues processed: 153
  average time/residue: 0.1042
  time to fit residues: 19.9971
Evaluate side-chains
  156 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  125 LYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  128 ARG
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:   40.0000
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:   20.0000
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.183501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.150637 restraints weight = 11131.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 2.33
r_work: 0.3723 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7935  Z= 0.209
  Angle     :  0.546  11.441  11081  Z= 0.298
  Chirality :  0.042   0.326   1284
  Planarity :  0.004   0.040   1057
  Dihedral  : 18.871 162.439   2129
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.57 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 24.76 %
    Favored  : 67.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.09 (0.32), residues: 682
  helix:  1.72 (0.27), residues: 316
  sheet: -0.94 (0.46), residues: 126
  loop : -2.03 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.021   0.002   PHE A 139 
 TRP   0.006   0.001   TRP A 206 
 HIS   0.006   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.21 ( 7935)
  covalent geometry    : angle       0.54622 /  0.30 (11081)
  hydrogen bonds       : bond        0.05570 /  3.85 (  396)
  hydrogen bonds       : angle       4.33389 /  3.19 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7662 (mmm-85)
REVERT: A   53 GLU cc_start: 0.7459 (tt0) cc_final: 0.5909 (tt0)
REVERT: A  134 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7191 (mmtt)
REVERT: A  136 ASP cc_start: 0.7482 (p0) cc_final: 0.7213 (p0)
REVERT: A  180 MET cc_start: 0.6930 (mmt) cc_final: 0.6647 (mmt)
REVERT: A  184 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7437 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8191 (ptpt)
REVERT: A  263 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7565 (ttm170)
REVERT: A  280 LYS cc_start: 0.8000 (tttt) cc_final: 0.7626 (mttt)
REVERT: B   57 ASP cc_start: 0.6910 (m-30) cc_final: 0.6644 (m-30)
REVERT: B   91 VAL cc_start: 0.7891 (t) cc_final: 0.7656 (p)
REVERT: B  139 PHE cc_start: 0.7716 (p90) cc_final: 0.7224 (p90)
REVERT: B  146 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5878 (tt)
REVERT: B  198 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: B  232 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6844 (mm-30)
REVERT: B  241 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7713 (tmtt)
  outliers start: 46
  outliers final: 32
  residues processed: 159
  average time/residue: 0.1038
  time to fit residues: 20.7575
Evaluate side-chains
  166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  351 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:   20.0000
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.185582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.153169 restraints weight = 11066.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.32
r_work: 0.3757 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7935  Z= 0.137
  Angle     :  0.499  11.229  11081  Z= 0.270
  Chirality :  0.039   0.301   1284
  Planarity :  0.003   0.042   1057
  Dihedral  : 18.854 160.865   2127
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.40 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 25.73 %
    Favored  : 68.45 %
  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:  0.16 (0.32), residues: 682
  helix:  1.94 (0.27), residues: 312
  sheet: -0.84 (0.47), residues: 126
  loop : -1.84 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 184 
 TYR   0.016   0.001   TYR B 353 
 PHE   0.018   0.002   PHE B 311 
 TRP   0.011   0.001   TRP B 342 
 HIS   0.003   0.001   HIS B 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.14 ( 7935)
  covalent geometry    : angle       0.49884 /  0.27 (11081)
  hydrogen bonds       : bond        0.05158 /  3.58 (  396)
  hydrogen bonds       : angle       4.17477 /  3.09 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7295 (ptmt) cc_final: 0.6880 (ttpp)
REVERT: A   53 GLU cc_start: 0.7379 (tt0) cc_final: 0.5820 (tt0)
REVERT: A  134 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7138 (mmtt)
REVERT: A  136 ASP cc_start: 0.7465 (p0) cc_final: 0.7200 (p0)
REVERT: A  180 MET cc_start: 0.6865 (mmt) cc_final: 0.6602 (mmt)
REVERT: A  184 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7148 (mtp85)
REVERT: A  214 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8136 (ptpt)
REVERT: A  263 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7530 (ttm170)
REVERT: A  280 LYS cc_start: 0.8024 (tttt) cc_final: 0.7599 (ttmm)
REVERT: B   57 ASP cc_start: 0.6819 (m-30) cc_final: 0.6565 (m-30)
REVERT: B   91 VAL cc_start: 0.7909 (t) cc_final: 0.7675 (p)
REVERT: B  139 PHE cc_start: 0.7706 (p90) cc_final: 0.7235 (p90)
REVERT: B  198 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7016 (tm-30)
REVERT: B  232 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6759 (mm-30)
REVERT: B  241 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7680 (tmtt)
  outliers start: 36
  outliers final: 23
  residues processed: 151
  average time/residue: 0.0866
  time to fit residues: 16.4610
Evaluate side-chains
  154 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0370
   chunk 65 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 59 optimal weight:   40.0000
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   8 HIS
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.185417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152851 restraints weight = 11085.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.33
r_work: 0.3751 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7935  Z= 0.149
  Angle     :  0.499  11.053  11081  Z= 0.272
  Chirality :  0.039   0.304   1284
  Planarity :  0.003   0.042   1057
  Dihedral  : 18.819 161.464   2127
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.69 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 26.21 %
    Favored  : 67.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.17 (0.32), residues: 682
  helix:  2.00 (0.27), residues: 312
  sheet: -0.88 (0.46), residues: 126
  loop : -1.88 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.017   0.002   PHE A  39 
 TRP   0.012   0.001   TRP B 342 
 HIS   0.009   0.001   HIS B   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.15 ( 7935)
  covalent geometry    : angle       0.49863 /  0.27 (11081)
  hydrogen bonds       : bond        0.05132 /  3.56 (  396)
  hydrogen bonds       : angle       4.13249 /  3.06 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7310 (ptmt) cc_final: 0.6884 (ttpp)
REVERT: A   53 GLU cc_start: 0.7393 (tt0) cc_final: 0.5830 (tt0)
REVERT: A  134 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7147 (mmtt)
REVERT: A  136 ASP cc_start: 0.7466 (p0) cc_final: 0.7211 (p0)
REVERT: A  180 MET cc_start: 0.6869 (mmt) cc_final: 0.6590 (mmt)
REVERT: A  184 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7159 (mtp85)
REVERT: A  214 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8148 (ptpt)
REVERT: A  263 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7532 (ttm170)
REVERT: A  280 LYS cc_start: 0.8037 (tttt) cc_final: 0.7599 (ttmm)
REVERT: B   57 ASP cc_start: 0.6818 (m-30) cc_final: 0.6562 (m-30)
REVERT: B   91 VAL cc_start: 0.7913 (t) cc_final: 0.7685 (p)
REVERT: B  139 PHE cc_start: 0.7678 (p90) cc_final: 0.7219 (p90)
REVERT: B  198 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7005 (tm-30)
REVERT: B  232 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6755 (mm-30)
REVERT: B  241 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7680 (tmtt)
  outliers start: 37
  outliers final: 29
  residues processed: 147
  average time/residue: 0.0974
  time to fit residues: 17.9342
Evaluate side-chains
  160 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:   40.0000
   chunk 53 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.185512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.153187 restraints weight = 10980.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.31
r_work: 0.3762 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7935  Z= 0.137
  Angle     :  0.489  10.909  11081  Z= 0.266
  Chirality :  0.039   0.298   1284
  Planarity :  0.003   0.042   1057
  Dihedral  : 18.804 161.310   2127
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.40 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 26.70 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.25 (0.32), residues: 682
  helix:  2.04 (0.27), residues: 312
  sheet: -0.82 (0.47), residues: 126
  loop : -1.83 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.019   0.002   PHE B 311 
 TRP   0.014   0.001   TRP B 342 
 HIS   0.004   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 ( 7935)
  covalent geometry    : angle       0.48946 /  0.27 (11081)
  hydrogen bonds       : bond        0.05028 /  3.49 (  396)
  hydrogen bonds       : angle       4.06949 /  3.01 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7399 (tt0) cc_final: 0.5828 (tt0)
REVERT: A  134 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7148 (mmtt)
REVERT: A  136 ASP cc_start: 0.7487 (p0) cc_final: 0.7226 (p0)
REVERT: A  180 MET cc_start: 0.6829 (mmt) cc_final: 0.6552 (mmt)
REVERT: A  184 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7188 (mtp85)
REVERT: A  214 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8144 (ptpt)
REVERT: A  263 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7517 (ttm170)
REVERT: A  280 LYS cc_start: 0.8041 (tttt) cc_final: 0.7613 (ttmm)
REVERT: B   57 ASP cc_start: 0.6796 (m-30) cc_final: 0.6545 (m-30)
REVERT: B   91 VAL cc_start: 0.7913 (t) cc_final: 0.7682 (p)
REVERT: B  139 PHE cc_start: 0.7659 (p90) cc_final: 0.7196 (p90)
REVERT: B  184 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7437 (ptt-90)
REVERT: B  198 GLN cc_start: 0.7399 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: B  232 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6741 (mm-30)
REVERT: B  241 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7656 (tmtt)
  outliers start: 36
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0983
  time to fit residues: 17.6315
Evaluate side-chains
  159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0060
   chunk 64 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0970
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.7196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.185867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.153638 restraints weight = 11068.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.31
r_work: 0.3767 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7935  Z= 0.132
  Angle     :  0.495  11.014  11081  Z= 0.268
  Chirality :  0.038   0.294   1284
  Planarity :  0.003   0.040   1057
  Dihedral  : 18.785 161.209   2127
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.40 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 27.51 %
    Favored  : 66.83 %
  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:  0.25 (0.32), residues: 682
  helix:  2.06 (0.27), residues: 313
  sheet: -0.83 (0.47), residues: 126
  loop : -1.86 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.023   0.002   PHE B 311 
 TRP   0.020   0.001   TRP B 342 
 HIS   0.004   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 ( 7935)
  covalent geometry    : angle       0.49510 /  0.27 (11081)
  hydrogen bonds       : bond        0.04962 /  3.44 (  396)
  hydrogen bonds       : angle       4.00193 /  2.95 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7428 (tt0) cc_final: 0.5883 (tt0)
REVERT: A  134 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7143 (mmtt)
REVERT: A  136 ASP cc_start: 0.7495 (p0) cc_final: 0.7224 (p0)
REVERT: A  180 MET cc_start: 0.6789 (mmt) cc_final: 0.6544 (mmt)
REVERT: A  184 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7201 (mtp85)
REVERT: A  214 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8149 (ptpt)
REVERT: A  263 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7467 (ttp-110)
REVERT: B   57 ASP cc_start: 0.6780 (m-30) cc_final: 0.6523 (m-30)
REVERT: B   91 VAL cc_start: 0.7913 (t) cc_final: 0.7687 (p)
REVERT: B  139 PHE cc_start: 0.7648 (p90) cc_final: 0.7210 (p90)
REVERT: B  198 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7006 (tm-30)
REVERT: B  232 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6739 (mm-30)
REVERT: B  241 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7657 (tmtt)
REVERT: B  315 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.7148 (m-70)
  outliers start: 35
  outliers final: 31
  residues processed: 147
  average time/residue: 0.0961
  time to fit residues: 17.5912
Evaluate side-chains
  165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.185848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.153666 restraints weight = 11059.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 2.32
r_work: 0.3771 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7935  Z= 0.136
  Angle     :  0.506  11.706  11081  Z= 0.272
  Chirality :  0.039   0.292   1284
  Planarity :  0.003   0.041   1057
  Dihedral  : 18.770 161.089   2123
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.69 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 27.02 %
    Favored  : 67.31 %
  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:  0.29 (0.32), residues: 682
  helix:  2.08 (0.27), residues: 312
  sheet: -0.79 (0.47), residues: 126
  loop : -1.82 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.025   0.002   PHE B 311 
 TRP   0.025   0.001   TRP B 342 
 HIS   0.004   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.14 ( 7935)
  covalent geometry    : angle       0.50611 /  0.27 (11081)
  hydrogen bonds       : bond        0.04939 /  3.41 (  396)
  hydrogen bonds       : angle       3.99414 /  2.95 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7437 (tt0) cc_final: 0.5869 (tt0)
REVERT: A  134 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7152 (mmtt)
REVERT: A  136 ASP cc_start: 0.7496 (p0) cc_final: 0.7227 (p0)
REVERT: A  180 MET cc_start: 0.6739 (mmt) cc_final: 0.6494 (mmt)
REVERT: A  184 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7211 (mtp85)
REVERT: A  263 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7472 (ttp-110)
REVERT: B   57 ASP cc_start: 0.6769 (m-30) cc_final: 0.6515 (m-30)
REVERT: B   91 VAL cc_start: 0.7922 (t) cc_final: 0.7702 (p)
REVERT: B  139 PHE cc_start: 0.7652 (p90) cc_final: 0.7219 (p90)
REVERT: B  198 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7030 (tm-30)
REVERT: B  232 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6733 (mm-30)
REVERT: B  241 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7668 (tmtt)
REVERT: B  315 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.7172 (m-70)
REVERT: B  342 TRP cc_start: 0.8266 (m100) cc_final: 0.8020 (m100)
  outliers start: 35
  outliers final: 31
  residues processed: 145
  average time/residue: 0.0996
  time to fit residues: 17.9818
Evaluate side-chains
  162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.185644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.153301 restraints weight = 11037.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.31
r_work: 0.3762 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7935  Z= 0.144
  Angle     :  0.513  10.608  11081  Z= 0.277
  Chirality :  0.039   0.292   1284
  Planarity :  0.004   0.044   1057
  Dihedral  : 18.770 161.142   2123
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.55 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 27.18 %
    Favored  : 67.15 %
  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:  0.28 (0.32), residues: 682
  helix:  2.08 (0.27), residues: 312
  sheet: -0.84 (0.46), residues: 132
  loop : -1.82 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.027   0.002   PHE B 311 
 TRP   0.024   0.001   TRP B 342 
 HIS   0.004   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 ( 7935)
  covalent geometry    : angle       0.51303 /  0.28 (11081)
  hydrogen bonds       : bond        0.04974 /  3.43 (  396)
  hydrogen bonds       : angle       3.99602 /  2.95 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7425 (tt0) cc_final: 0.5877 (tt0)
REVERT: A  134 LYS cc_start: 0.7409 (mmtt) cc_final: 0.7141 (mmtt)
REVERT: A  136 ASP cc_start: 0.7496 (p0) cc_final: 0.7231 (p0)
REVERT: A  180 MET cc_start: 0.6723 (mmt) cc_final: 0.6491 (mmt)
REVERT: A  184 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7207 (mtp85)
REVERT: A  263 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7474 (ttp-110)
REVERT: B   57 ASP cc_start: 0.6799 (m-30) cc_final: 0.6540 (m-30)
REVERT: B   91 VAL cc_start: 0.7912 (t) cc_final: 0.7700 (p)
REVERT: B  139 PHE cc_start: 0.7654 (p90) cc_final: 0.7239 (p90)
REVERT: B  198 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7021 (tm-30)
REVERT: B  232 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6725 (mm-30)
REVERT: B  241 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7707 (tmtt)
REVERT: B  315 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7154 (m-70)
REVERT: B  342 TRP cc_start: 0.8327 (m100) cc_final: 0.7992 (m100)
  outliers start: 35
  outliers final: 31
  residues processed: 147
  average time/residue: 0.0943
  time to fit residues: 17.4848
Evaluate side-chains
  163 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  315 HIS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.185491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.153169 restraints weight = 10983.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.29
r_work: 0.3761 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7935  Z= 0.150
  Angle     :  0.518  10.899  11081  Z= 0.281
  Chirality :  0.039   0.292   1284
  Planarity :  0.004   0.057   1057
  Dihedral  : 18.774 161.288   2123
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.55 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 27.18 %
    Favored  : 66.83 %
  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:  0.26 (0.32), residues: 682
  helix:  2.05 (0.27), residues: 312
  sheet: -0.87 (0.46), residues: 132
  loop : -1.80 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG B 184 
 TYR   0.015   0.001   TYR B 353 
 PHE   0.028   0.002   PHE B 311 
 TRP   0.024   0.001   TRP B 342 
 HIS   0.005   0.001   HIS A   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 7935)
  covalent geometry    : angle       0.51849 /  0.28 (11081)
  hydrogen bonds       : bond        0.05001 /  3.45 (  396)
  hydrogen bonds       : angle       4.01607 /  2.96 ( 1126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1374.04 seconds
wall clock time: 24 minutes 13.95 seconds (1453.95 seconds total)