Starting phenix.real_space_refine
on Tue Mar 11 22:17:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cth_26990/03_2025/8cth_26990.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      74      5.49       5
     S      22      5.16       5
     C    3250      2.51       5
     N     969      2.21       5
     O    1229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5544
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1750
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 199}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2175
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 8, 'TRANS': 269}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1593
          Classifications: {'RNA': 74}
          Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p': 10, 'rna3p_pur': 32, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 9, 'rna3p': 64}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 5
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.98
  Number of scatterers: 5544
  At special positions: 0
  Unit cell: (81, 100.44, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P      74     15.00
     O    1229      8.00
     N     969      7.00
     C    3250      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: 2.20
  Conformation dependent library (CDL) restraints added in 477.8 milliseconds
  

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  926

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      18.4% alpha, 31.1% beta
      20 base pairs and 39 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 44
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.500A  pdb=" N   GLU A  48 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 3.866A  pdb=" N   VAL A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A  93 " --> pdb=" O   GLY A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 125
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 3.539A  pdb=" N   PHE A 148 " --> pdb=" O   HIS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.904A  pdb=" N   LYS A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG A 174 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 3.599A  pdb=" N   HIS A 210 " --> pdb=" O   TRP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 3.514A  pdb=" N   GLY A 232 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 234 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 137
      removed outlier: 6.525A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   GLY A 105 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A 102 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ARG A 258 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 193 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   PHE A 256 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   TYR A 195 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ALA A 254 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE A 197 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   PHE A 252 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10
    Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 10
      removed outlier: 3.673A  pdb=" N   PHE B  22 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR B  38 " --> pdb=" O   PHE B  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 69
      removed outlier: 4.133A  pdb=" N   ALA B  66 " --> pdb=" O   THR B  79 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   PHE B  76 " --> pdb=" O   PHE B  88 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER B  97 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110
      removed outlier: 3.975A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR B 109 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153
      removed outlier: 6.588A  pdb=" N   ALA B 163 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   VAL B 151 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   VAL B 153 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   PHE B 159 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LYS B 168 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE B 169 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   VAL B 171 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.897A  pdb=" N   SER B 206 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 252
      removed outlier: 4.199A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 268 " --> pdb=" O   GLN B 285 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   GLN B 285 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ILE B 270 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG B 283 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 292 through 297
      removed outlier: 3.606A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU B 303 " --> pdb=" O   TYR B 317 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 305 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    303 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      39 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 2.30 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: 1036
        1.33 -     1.45: 1792
        1.45 -     1.57: 2826
        1.57 -     1.69: 147
        1.69 -     1.81: 29
  Bond restraints: 5830
  Sorted by residual:
  bond pdb=" C2  SAH A 301 "
       pdb=" N3  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.48e+00
  bond pdb=" C8  SAH A 301 "
       pdb=" N7  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.299  1.352 -0.053 2.00e-02 2.50e+03 6.89e+00
  bond pdb=" C2  SAH A 301 "
       pdb=" N1  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.377 -0.047 2.00e-02 2.50e+03 5.52e+00
  bond pdb=" C6  SAH A 301 "
       pdb=" N1  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.338  1.377 -0.039 2.00e-02 2.50e+03 3.71e+00
  bond pdb=" C1' SAH A 301 "
       pdb=" N9  SAH A 301 "
    ideal  model  delta    sigma   weight residual
    1.440  1.473 -0.033 2.00e-02 2.50e+03 2.71e+00
  ... (remaining 5825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 8161
        2.50 -     5.01: 89
        5.01 -     7.51: 9
        7.51 -    10.01: 8
       10.01 -    12.52: 1
  Bond angle restraints: 8268
  Sorted by residual:
  angle pdb=" CG  SAH A 301 "
        pdb=" SD  SAH A 301 "
        pdb=" C5' SAH A 301 "
      ideal   model   delta    sigma   weight residual
     101.77   89.25   12.52 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" C8  7MG C  46 "
        pdb=" N7  7MG C  46 "
        pdb=" CM7 7MG C  46 "
      ideal   model   delta    sigma   weight residual
     112.82  122.50   -9.68 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" C5  7MG C  46 "
        pdb=" N7  7MG C  46 "
        pdb=" CM7 7MG C  46 "
      ideal   model   delta    sigma   weight residual
     118.03  127.67   -9.64 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" O   SAH A 301 "
        pdb=" C   SAH A 301 "
        pdb=" OXT SAH A 301 "
      ideal   model   delta    sigma   weight residual
     126.79  117.77    9.02 3.00e+00 1.11e-01 9.03e+00
  angle pdb=" C2  SAH A 301 "
        pdb=" N3  SAH A 301 "
        pdb=" C4  SAH A 301 "
      ideal   model   delta    sigma   weight residual
     111.67  120.42   -8.75 3.00e+00 1.11e-01 8.50e+00
  ... (remaining 8263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.48: 3083
       19.48 -    38.95: 292
       38.95 -    58.42: 116
       58.42 -    77.90: 72
       77.90 -    97.37: 5
  Dihedral angle restraints: 3568
    sinusoidal: 2139
      harmonic: 1429
  Sorted by residual:
  dihedral pdb=" CA  ARG B  89 "
           pdb=" C   ARG B  89 "
           pdb=" N   THR B  90 "
           pdb=" CA  THR B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.34  -18.66     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" OP2 PSU C  39 "
           pdb=" P   PSU C  39 "
           pdb=" O5' PSU C  39 "
           pdb=" C5' PSU C  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      86.61 -176.02  -97.37     1      3.00e+01 1.11e-03 1.20e+01
  dihedral pdb=" OP2 PSU C  55 "
           pdb=" P   PSU C  55 "
           pdb=" O5' PSU C  55 "
           pdb=" C5' PSU C  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
      86.61  179.26  -92.65     1      3.00e+01 1.11e-03 1.12e+01
  ... (remaining 3565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 746
       0.040 -    0.080: 154
       0.080 -    0.120: 57
       0.120 -    0.160: 9
       0.160 -    0.200: 1
  Chirality restraints: 967
  Sorted by residual:
  chirality pdb=" C1'   U C  59 "
            pdb=" O4'   U C  59 "
            pdb=" C2'   U C  59 "
            pdb=" N1    U C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE A 259 "
            pdb=" N   ILE A 259 "
            pdb=" C   ILE A 259 "
            pdb=" CB  ILE A 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 964 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 163 "    0.066 5.00e-02 4.00e+02   1.00e-01 1.60e+01
        pdb=" N   PRO A 164 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO A 164 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 164 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  19 "    0.026 2.00e-02 2.50e+03   1.12e-02 3.79e+00
        pdb=" N9    G C  19 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8    G C  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  19 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G C  19 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G C  19 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G C  19 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    G C  19 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  19 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G C  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G C  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G C  19 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  59 "   -0.022 2.00e-02 2.50e+03   1.17e-02 3.08e+00
        pdb=" N1    U C  59 "    0.026 2.00e-02 2.50e+03
        pdb=" C2    U C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" O2    U C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    U C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" O4    U C  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    U C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U C  59 "    0.005 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1174
        2.79 -     3.31: 4868
        3.31 -     3.84: 10012
        3.84 -     4.37: 11726
        4.37 -     4.90: 18141
  Nonbonded interactions: 45921
  Sorted by model distance:
  nonbonded pdb=" O2' 1MA C  58 "
            pdb=" OP2   C C  60 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" NZ  LYS B  83 "
            pdb=" OP1 5MU C  54 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OH  TYR A  50 "
            pdb=" O   ILE A 103 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG  SER B 146 "
            pdb=" OD2 ASP B 166 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG  SER B 146 "
            pdb=" OD2 ASP B 164 "
     model   vdw
     2.367 3.040
  ... (remaining 45916 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.950
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6496
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      :  0.003   0.058   5830  Z= 0.201
  Angle     :  0.677  12.516   8268  Z= 0.304
  Chirality :  0.038   0.200    967
  Planarity :  0.005   0.100    776
  Dihedral  : 19.263  97.372   2642
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.93 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.34), residues: 482
  helix: -0.05 (0.58), residues: 65
  sheet: -0.84 (0.43), residues: 147
  loop : -1.55 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 206 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.008   0.001   PHE A 159 
 TYR   0.014   0.002   TYR A 115 
 ARG   0.004   0.000   ARG A 124 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   30 MET cc_start: 0.5957 (mpp) cc_final: 0.5019 (mtt)
REVERT: B  157 ASP cc_start: 0.6945 (m-30) cc_final: 0.6048 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2356
  time to fit residues: 15.8641
Evaluate side-chains
  46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0670
   chunk 49 optimal weight:    8.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.262242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.221497 restraints weight = 7045.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.4640 rms_B_bonded: 1.78
r_work: 0.4431 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5830  Z= 0.172
  Angle     :  0.546   4.961   8268  Z= 0.269
  Chirality :  0.038   0.207    967
  Planarity :  0.004   0.064    776
  Dihedral  : 17.983  78.617   1728
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 18.91 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.36), residues: 482
  helix:  1.05 (0.64), residues: 67
  sheet: -0.68 (0.42), residues: 160
  loop : -1.29 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 206 
 HIS   0.002   0.001   HIS A  33 
 PHE   0.009   0.001   PHE B 183 
 TYR   0.010   0.001   TYR B 218 
 ARG   0.004   0.000   ARG B 283 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5616 (mpt-90)
REVERT: B  117 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8756 (p)
REVERT: B  133 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7017 (tm-30)
REVERT: B  145 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6616 (tt)
REVERT: B  157 ASP cc_start: 0.6989 (m-30) cc_final: 0.6061 (m-30)
REVERT: B  269 TYR cc_start: 0.6422 (m-10) cc_final: 0.5974 (m-10)
  outliers start: 16
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1902
  time to fit residues: 17.4774
Evaluate side-chains
  62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  207 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.6898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.258537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.216703 restraints weight = 7129.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4597 rms_B_bonded: 1.82
r_work: 0.4404 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6635
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5830  Z= 0.182
  Angle     :  0.550   6.300   8268  Z= 0.269
  Chirality :  0.039   0.229    967
  Planarity :  0.004   0.047    776
  Dihedral  : 17.899  75.613   1728
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 19.39 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.37), residues: 482
  helix:  1.32 (0.66), residues: 68
  sheet: -0.68 (0.41), residues: 172
  loop : -1.25 (0.35), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 216 
 HIS   0.002   0.001   HIS A 233 
 PHE   0.009   0.001   PHE B 183 
 TYR   0.012   0.001   TYR A 115 
 ARG   0.005   0.000   ARG B 139 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ILE cc_start: 0.8786 (mm) cc_final: 0.8521 (mt)
REVERT: A  124 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5887 (mpt-90)
REVERT: A  142 MET cc_start: 0.7576 (mmm) cc_final: 0.7075 (mmm)
REVERT: A  211 PHE cc_start: 0.4022 (OUTLIER) cc_final: 0.3666 (m-80)
REVERT: B  117 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8864 (p)
REVERT: B  133 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6976 (tm-30)
REVERT: B  145 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6493 (tt)
  outliers start: 22
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1644
  time to fit residues: 14.8872
Evaluate side-chains
  67 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.254502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.213966 restraints weight = 7213.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.4598 rms_B_bonded: 1.68
r_work: 0.4402 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5830  Z= 0.206
  Angle     :  0.572   5.873   8268  Z= 0.281
  Chirality :  0.039   0.244    967
  Planarity :  0.004   0.047    776
  Dihedral  : 17.900  74.945   1728
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 20.33 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.36), residues: 482
  helix:  1.36 (0.66), residues: 68
  sheet: -0.64 (0.42), residues: 154
  loop : -1.47 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 216 
 HIS   0.005   0.001   HIS A  33 
 PHE   0.010   0.001   PHE B 183 
 TYR   0.011   0.001   TYR A 115 
 ARG   0.003   0.000   ARG A 124 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 49
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ASP cc_start: 0.5987 (t0) cc_final: 0.5778 (t0)
REVERT: A  124 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5878 (mpt-90)
REVERT: A  142 MET cc_start: 0.7649 (mmm) cc_final: 0.7164 (mtp)
REVERT: A  169 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6946 (p)
REVERT: A  211 PHE cc_start: 0.3994 (OUTLIER) cc_final: 0.3471 (m-80)
REVERT: B  117 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8855 (p)
REVERT: B  145 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6476 (tt)
  outliers start: 23
  outliers final: 16
  residues processed: 66
  average time/residue: 0.1764
  time to fit residues: 15.5158
Evaluate side-chains
  64 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.254030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.211326 restraints weight = 7076.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 1.66
r_work: 0.4395 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5830  Z= 0.300
  Angle     :  0.646   5.995   8268  Z= 0.321
  Chirality :  0.042   0.280    967
  Planarity :  0.005   0.054    776
  Dihedral  : 18.054  83.193   1728
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 19.39 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.35), residues: 482
  helix:  1.13 (0.67), residues: 68
  sheet: -1.07 (0.43), residues: 149
  loop : -1.72 (0.31), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 216 
 HIS   0.004   0.001   HIS A 204 
 PHE   0.016   0.002   PHE B 183 
 TYR   0.014   0.002   TYR A 115 
 ARG   0.003   0.001   ARG B 103 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ASP cc_start: 0.5937 (t0) cc_final: 0.5702 (t0)
REVERT: A  124 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6309 (mpt-90)
REVERT: A  142 MET cc_start: 0.7727 (mmm) cc_final: 0.7453 (mtp)
REVERT: A  169 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6996 (p)
REVERT: A  211 PHE cc_start: 0.4176 (OUTLIER) cc_final: 0.3465 (m-80)
REVERT: A  257 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7673 (ttm170)
REVERT: B  145 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6636 (tt)
REVERT: B  164 ASP cc_start: 0.7637 (t70) cc_final: 0.7357 (t70)
  outliers start: 22
  outliers final: 16
  residues processed: 65
  average time/residue: 0.1772
  time to fit residues: 15.2188
Evaluate side-chains
  61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0040
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0030
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.4202

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.260494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.219769 restraints weight = 7087.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.4667 rms_B_bonded: 1.69
r_work: 0.4476 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5830  Z= 0.144
  Angle     :  0.535   5.836   8268  Z= 0.262
  Chirality :  0.038   0.264    967
  Planarity :  0.004   0.047    776
  Dihedral  : 17.813  73.968   1728
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 20.57 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.36), residues: 482
  helix:  1.40 (0.68), residues: 68
  sheet: -0.89 (0.41), residues: 164
  loop : -1.31 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 206 
 HIS   0.002   0.001   HIS A  33 
 PHE   0.010   0.001   PHE A 159 
 TYR   0.015   0.001   TYR A 115 
 ARG   0.003   0.000   ARG B 219 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  114 ASP cc_start: 0.5819 (t0) cc_final: 0.5617 (t0)
REVERT: A  124 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5616 (mpt-90)
REVERT: A  142 MET cc_start: 0.7686 (mmm) cc_final: 0.7372 (mtp)
REVERT: A  211 PHE cc_start: 0.3972 (OUTLIER) cc_final: 0.3534 (m-80)
REVERT: B  145 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6496 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 60
  average time/residue: 0.1794
  time to fit residues: 14.1391
Evaluate side-chains
  54 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 50 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7340

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.257593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.215490 restraints weight = 7147.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.4598 rms_B_bonded: 1.65
r_work: 0.4410 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5830  Z= 0.194
  Angle     :  0.561   5.666   8268  Z= 0.275
  Chirality :  0.039   0.249    967
  Planarity :  0.004   0.054    776
  Dihedral  : 17.846  74.662   1728
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 20.80 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.36), residues: 482
  helix:  1.40 (0.69), residues: 68
  sheet: -0.85 (0.42), residues: 154
  loop : -1.41 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.010   0.001   PHE A 159 
 TYR   0.010   0.001   TYR B 218 
 ARG   0.003   0.000   ARG A 124 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  124 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5824 (mpt-90)
REVERT: A  142 MET cc_start: 0.7715 (mmm) cc_final: 0.7452 (mtp)
REVERT: A  169 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6942 (p)
REVERT: A  211 PHE cc_start: 0.3950 (OUTLIER) cc_final: 0.3460 (m-80)
REVERT: B  145 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6286 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 59
  average time/residue: 0.1578
  time to fit residues: 12.6270
Evaluate side-chains
  60 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.254739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.211442 restraints weight = 7057.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4572 rms_B_bonded: 1.65
r_work: 0.4372 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5830  Z= 0.258
  Angle     :  0.618   6.179   8268  Z= 0.306
  Chirality :  0.042   0.274    967
  Planarity :  0.005   0.051    776
  Dihedral  : 17.982  79.854   1728
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.09 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.35), residues: 482
  helix:  1.24 (0.68), residues: 68
  sheet: -1.15 (0.43), residues: 143
  loop : -1.67 (0.31), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 216 
 HIS   0.003   0.001   HIS A 204 
 PHE   0.013   0.002   PHE B 183 
 TYR   0.018   0.002   TYR A  87 
 ARG   0.003   0.000   ARG A 124 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  124 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.6049 (mpt-90)
REVERT: A  142 MET cc_start: 0.7759 (mmm) cc_final: 0.7492 (mtp)
REVERT: A  169 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7034 (p)
REVERT: A  211 PHE cc_start: 0.4060 (OUTLIER) cc_final: 0.3463 (m-80)
REVERT: B  145 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6470 (tt)
REVERT: B  164 ASP cc_start: 0.7666 (t70) cc_final: 0.7352 (t70)
  outliers start: 22
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1820
  time to fit residues: 14.2054
Evaluate side-chains
  61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.257642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.216825 restraints weight = 7124.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4621 rms_B_bonded: 1.69
r_work: 0.4409 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5830  Z= 0.182
  Angle     :  0.560   6.424   8268  Z= 0.275
  Chirality :  0.039   0.269    967
  Planarity :  0.004   0.049    776
  Dihedral  : 17.868  73.978   1728
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.80 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.36), residues: 482
  helix:  1.31 (0.68), residues: 68
  sheet: -1.04 (0.42), residues: 148
  loop : -1.49 (0.32), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.009   0.001   PHE A 159 
 TYR   0.014   0.001   TYR A 115 
 ARG   0.006   0.000   ARG A 168 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  124 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5817 (mpt-90)
REVERT: A  142 MET cc_start: 0.7775 (mmm) cc_final: 0.7482 (mtp)
REVERT: A  169 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7135 (p)
REVERT: A  211 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3510 (m-80)
REVERT: B  145 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6511 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 55
  average time/residue: 0.1583
  time to fit residues: 11.7913
Evaluate side-chains
  59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0770
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0030
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.4950

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

Flipped N/Q/H residues before XYZ refinement:
A 233 HIS
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.258855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.218903 restraints weight = 7173.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4640 rms_B_bonded: 1.69
r_work: 0.4428 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5830  Z= 0.157
  Angle     :  0.537   6.376   8268  Z= 0.263
  Chirality :  0.038   0.248    967
  Planarity :  0.004   0.049    776
  Dihedral  : 17.804  73.949   1728
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.28 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.36), residues: 482
  helix:  1.42 (0.68), residues: 68
  sheet: -0.94 (0.40), residues: 159
  loop : -1.32 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 252 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.009   0.001   PHE A 159 
 TYR   0.010   0.001   TYR A  87 
 ARG   0.006   0.000   ARG A 168 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  124 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5624 (mpt-90)
REVERT: A  142 MET cc_start: 0.7744 (mmm) cc_final: 0.7417 (mtp)
REVERT: A  169 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7124 (p)
REVERT: A  211 PHE cc_start: 0.3944 (OUTLIER) cc_final: 0.3538 (m-80)
REVERT: B  133 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7066 (tm-30)
REVERT: B  145 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6417 (tt)
REVERT: B  164 ASP cc_start: 0.7453 (t70) cc_final: 0.7054 (t70)
  outliers start: 18
  outliers final: 14
  residues processed: 57
  average time/residue: 0.1615
  time to fit residues: 12.4725
Evaluate side-chains
  60 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  258 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0030
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.259134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.218746 restraints weight = 7281.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.4645 rms_B_bonded: 1.93
r_work: 0.4414 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5830  Z= 0.165
  Angle     :  0.541   6.495   8268  Z= 0.265
  Chirality :  0.038   0.250    967
  Planarity :  0.004   0.059    776
  Dihedral  : 17.806  73.952   1728
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.75 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.36), residues: 482
  helix:  1.45 (0.68), residues: 68
  sheet: -0.97 (0.39), residues: 165
  loop : -1.14 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 216 
 HIS   0.002   0.001   HIS B 144 
 PHE   0.011   0.001   PHE A 159 
 TYR   0.016   0.001   TYR A  87 
 ARG   0.006   0.000   ARG A 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2900.72 seconds
wall clock time: 50 minutes 26.52 seconds (3026.52 seconds total)