Starting phenix.real_space_refine
on Thu Jul  2 03:09:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enc_19831/07_2026/9enc_19831.cif"
  }
  resolution = 3.36
  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=   0.030
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      30      5.16       5
     C    3699      2.51       5
     N    1089      2.21       5
     O    1357      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6249
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2304
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2356
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1589
          Classifications: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 15, 'rna3p': 59}
  Time building chain proxies: 0.99, per 1000 atoms: 0.16
  Number of scatterers: 6249
  At special positions: 0
  Unit cell: (102.318, 127.686, 65.9568, 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      30     16.00
     P      74     15.00
     O    1357      8.00
     N    1089      7.00
     C    3699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 114 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 327 " distance=2.03

  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: 0.41
  Conformation dependent library (CDL) restraints added in 186.2 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      35.3% alpha, 25.1% beta
      22 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 100
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 3.924A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 3.766A  pdb=" N   TYR A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 3.746A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.503A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 159 through 168
      removed outlier: 3.925A  pdb=" N   VAL B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.667A  pdb=" N   GLN B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 3.791A  pdb=" N   CYS B 226 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.659A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 289 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.518A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 5.122A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A  63 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   HIS A  64 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA A  66 " --> pdb=" O   TRP A 177 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG A  68 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 6.346A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 11.007A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   LEU A 264 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 5.056A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113
      removed outlier: 7.226A  pdb=" N   SER B 122 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   ASP B 326 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   PHE B 124 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   LYS B 328 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 10.704A  pdb=" N   GLN B 126 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 199 " --> pdb=" O   CYS B 265 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU B 264 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN B 266 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL B 246 " --> pdb=" O   GLN B 266 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ALA B 244 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG B 239 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   HIS B 220 " --> pdb=" O   ARG B 239 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    516 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      58 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 0.74

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1690
        1.34 -     1.45: 1630
        1.45 -     1.57: 3030
        1.57 -     1.69: 148
        1.69 -     1.81: 48
  Bond restraints: 6546
  Sorted by residual:
  bond pdb=" C   GLU B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 8.40e-03 1.42e+04 4.65e+00
  bond pdb=" C   GLU A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.014 1.11e-02 8.12e+03 1.69e+00
  bond pdb=" C3'   G D  36 "
       pdb=" O3'   G D  36 "
    ideal  model  delta    sigma   weight residual
    1.427  1.443 -0.016 1.50e-02 4.44e+03 1.14e+00
  bond pdb=" CA  ASN A 232 "
       pdb=" C   ASN A 232 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.013 1.41e-02 5.03e+03 8.00e-01
  bond pdb=" O3'   G D  36 "
       pdb=" P     A D  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.620 -0.013 1.50e-02 4.44e+03 7.47e-01
  ... (remaining 6541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 9122
        2.07 -     4.14: 81
        4.14 -     6.20: 9
        6.20 -     8.27: 0
        8.27 -    10.34: 1
  Bond angle restraints: 9213
  Sorted by residual:
  angle pdb=" C1'   C D  48 "
        pdb=" N1    C D  48 "
        pdb=" C2    C D  48 "
      ideal   model   delta    sigma   weight residual
     118.80  123.62   -4.82 1.10e+00 8.26e-01 1.92e+01
  angle pdb=" N1    C D  48 "
        pdb=" C2    C D  48 "
        pdb=" O2    C D  48 "
      ideal   model   delta    sigma   weight residual
     118.90  121.29   -2.39 6.00e-01 2.78e+00 1.59e+01
  angle pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
      ideal   model   delta    sigma   weight residual
     120.20  125.79   -5.59 1.50e+00 4.44e-01 1.39e+01
  angle pdb=" C1'   U D  35 "
        pdb=" N1    U D  35 "
        pdb=" C2    U D  35 "
      ideal   model   delta    sigma   weight residual
     117.70  122.03   -4.33 1.20e+00 6.94e-01 1.30e+01
  angle pdb=" O3'   G D  36 "
        pdb=" P     A D  37 "
        pdb=" OP1   A D  37 "
      ideal   model   delta    sigma   weight residual
     108.00  118.34  -10.34 3.00e+00 1.11e-01 1.19e+01
  ... (remaining 9208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.20: 3647
       31.20 -    62.40: 282
       62.40 -    93.60: 79
       93.60 -   124.80: 2
      124.80 -   156.00: 4
  Dihedral angle restraints: 4014
    sinusoidal: 2349
      harmonic: 1665
  Sorted by residual:
  dihedral pdb=" O4'   U D  35 "
           pdb=" C1'   U D  35 "
           pdb=" N1    U D  35 "
           pdb=" C2    U D  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.00  156.00     1      1.50e+01 4.44e-03 8.16e+01
  dihedral pdb=" O4'   C D  48 "
           pdb=" C1'   C D  48 "
           pdb=" N1    C D  48 "
           pdb=" C2    C D  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -25.27 -134.73     1      1.50e+01 4.44e-03 7.27e+01
  dihedral pdb=" O4'   A D  37 "
           pdb=" C1'   A D  37 "
           pdb=" N9    A D  37 "
           pdb=" C4    A D  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  175.33   78.67     1      1.70e+01 3.46e-03 2.67e+01
  ... (remaining 4011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 870
       0.042 -    0.084: 148
       0.084 -    0.126: 40
       0.126 -    0.168: 3
       0.168 -    0.210: 2
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" P     A D  37 "
            pdb=" OP1   A D  37 "
            pdb=" OP2   A D  37 "
            pdb=" O5'   A D  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.62   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" C1'   A D  58 "
            pdb=" O4'   A D  58 "
            pdb=" C2'   A D  58 "
            pdb=" N9    A D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 907
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  32 "    0.026 2.00e-02 2.50e+03   1.32e-02 3.94e+00
        pdb=" N1    C D  32 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    C D  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C D  32 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C D  32 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C D  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  32 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  58 "   -0.017 2.00e-02 2.50e+03   8.90e-03 2.18e+00
        pdb=" N9    A D  58 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A D  58 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A D  58 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  58 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A D  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1    A D  58 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  58 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  58 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  58 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  44 "   -0.018 2.00e-02 2.50e+03   9.34e-03 1.96e+00
        pdb=" N1    C D  44 "    0.020 2.00e-02 2.50e+03
        pdb=" C2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    C D  44 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4    C D  44 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  44 "    0.004 2.00e-02 2.50e+03
  ... (remaining 904 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1073
        2.77 -     3.30: 5518
        3.30 -     3.83: 10864
        3.83 -     4.37: 12384
        4.37 -     4.90: 20070
  Nonbonded interactions: 49909
  Sorted by model distance:
  nonbonded pdb=" OP2   G D  45 "
            pdb=" N2    G D  45 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O2'   U D  35 "
            pdb=" OP1   A D  37 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER B 105 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O2'   A D   7 "
            pdb=" O2    C D  48 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" O   VAL A 318 "
     model   vdw
     2.305 3.040
  ... (remaining 49904 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 61 through 228 or resid 236 through 249 or resid 257 throu \ 
gh 369))
  selection = (chain 'B' and (resid 61 through 134 or resid 157 through 369))
}

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:             1.760
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.240
  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:             0.010
  Load rotamer database and sin/cos tables:0.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6548  Z= 0.144
  Angle     :  0.512  10.339   9217  Z= 0.362
  Chirality :  0.035   0.210   1063
  Planarity :  0.003   0.033    907
  Dihedral  : 21.396 156.003   2928
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 27.66 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.36), residues: 552
  helix:  1.24 (0.40), residues: 172
  sheet:  0.61 (0.57), residues: 87
  loop : -1.22 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.006   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.14 ( 6546)
  covalent geometry    : angle       0.51224 /  0.36 ( 9213)
  SS BOND              : bond        0.00164 /  0.10 (    2)
  SS BOND              : angle       0.66776 /  0.35 (    4)
  hydrogen bonds       : bond        0.19239 / 12.49 (  239)
  hydrogen bonds       : angle       6.40376 /  4.48 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  293 MET cc_start: 0.7799 (ttt) cc_final: 0.7593 (ttt)
REVERT: A  295 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (ttpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0754
  time to fit residues: 3.2110
Evaluate side-chains
  22 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.072806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.053116 restraints weight = 20889.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 3.09
r_work: 0.2968 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6548  Z= 0.139
  Angle     :  0.503  10.735   9217  Z= 0.280
  Chirality :  0.038   0.240   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.811 154.237   1796
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 25.85 %
    Favored  : 72.95 %
  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 (0.36), residues: 552
  helix:  2.13 (0.38), residues: 170
  sheet:  0.59 (0.56), residues: 91
  loop : -1.23 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 193 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.016   0.001   PHE B 320 
 TRP   0.018   0.002   TRP A 258 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 6546)
  covalent geometry    : angle       0.50313 /  0.28 ( 9213)
  SS BOND              : bond        0.00391 /  0.23 (    2)
  SS BOND              : angle       0.88674 /  0.47 (    4)
  hydrogen bonds       : bond        0.05806 /  3.90 (  239)
  hydrogen bonds       : angle       4.46398 /  3.18 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8469 (mpp) cc_final: 0.8125 (mmm)
REVERT: A  258 TRP cc_start: 0.8054 (t60) cc_final: 0.7355 (t60)
REVERT: A  293 MET cc_start: 0.7839 (ttt) cc_final: 0.7597 (ttm)
  outliers start: 6
  outliers final: 1
  residues processed: 26
  average time/residue: 0.0461
  time to fit residues: 1.8882
Evaluate side-chains
  22 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 110 ASN
B 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.070482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.050772 restraints weight = 20951.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.08
r_work: 0.2904 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   6548  Z= 0.253
  Angle     :  0.582  11.142   9217  Z= 0.318
  Chirality :  0.041   0.241   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.829 154.540   1792
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.05 %
    Favored  : 72.95 %
  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:  0.03 (0.36), residues: 552
  helix:  2.13 (0.38), residues: 167
  sheet:  0.12 (0.55), residues: 86
  loop : -1.30 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.017   0.002   TYR A 195 
 PHE   0.018   0.002   PHE B  94 
 TRP   0.010   0.002   TRP A 352 
 HIS   0.008   0.002   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00576 /  0.25 ( 6546)
  covalent geometry    : angle       0.58153 /  0.32 ( 9213)
  SS BOND              : bond        0.00540 /  0.32 (    2)
  SS BOND              : angle       1.20214 /  0.62 (    4)
  hydrogen bonds       : bond        0.06428 /  4.24 (  239)
  hydrogen bonds       : angle       4.52369 /  3.19 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8540 (mpp) cc_final: 0.8199 (mmm)
REVERT: A  258 TRP cc_start: 0.8219 (t60) cc_final: 0.7569 (t60)
REVERT: B   72 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8351 (mmm)
  outliers start: 15
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0577
  time to fit residues: 2.6006
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 58 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.071134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.051427 restraints weight = 20926.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.09
r_work: 0.2921 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6548  Z= 0.176
  Angle     :  0.504  10.792   9217  Z= 0.280
  Chirality :  0.039   0.240   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.796 154.855   1792
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.45 %
    Favored  : 74.15 %
  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:  0.06 (0.36), residues: 552
  helix:  2.19 (0.38), residues: 167
  sheet:  0.07 (0.56), residues: 84
  loop : -1.29 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.011   0.001   TYR A 195 
 PHE   0.017   0.001   PHE B 124 
 TRP   0.019   0.002   TRP B  74 
 HIS   0.004   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 6546)
  covalent geometry    : angle       0.50387 /  0.28 ( 9213)
  SS BOND              : bond        0.00475 /  0.28 (    2)
  SS BOND              : angle       1.11053 /  0.57 (    4)
  hydrogen bonds       : bond        0.05775 /  3.86 (  239)
  hydrogen bonds       : angle       4.24627 /  2.98 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 21
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8512 (mpp) cc_final: 0.8167 (mmm)
REVERT: A  229 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8361 (t70)
REVERT: A  258 TRP cc_start: 0.8206 (t60) cc_final: 0.7585 (t60)
REVERT: A  293 MET cc_start: 0.7787 (ttt) cc_final: 0.7468 (ttm)
  outliers start: 12
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0399
  time to fit residues: 1.9621
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 8 optimal weight:    0.1980
   chunk 60 optimal weight:   10.0000
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.071461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.051753 restraints weight = 21273.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.11
r_work: 0.2930 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6548  Z= 0.154
  Angle     :  0.479  10.408   9217  Z= 0.267
  Chirality :  0.038   0.235   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.762 155.168   1792
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 24.05 %
    Favored  : 74.35 %
  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:  0.12 (0.36), residues: 552
  helix:  2.27 (0.39), residues: 167
  sheet:  0.16 (0.56), residues: 84
  loop : -1.29 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.012   0.001   TYR A 216 
 PHE   0.015   0.001   PHE B 124 
 TRP   0.010   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 6546)
  covalent geometry    : angle       0.47904 /  0.27 ( 9213)
  SS BOND              : bond        0.00470 /  0.28 (    2)
  SS BOND              : angle       1.05235 /  0.53 (    4)
  hydrogen bonds       : bond        0.05499 /  3.69 (  239)
  hydrogen bonds       : angle       4.09045 /  2.87 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8529 (mpp) cc_final: 0.8181 (mmm)
REVERT: A  229 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8363 (t70)
REVERT: A  258 TRP cc_start: 0.8199 (t60) cc_final: 0.7617 (t60)
  outliers start: 8
  outliers final: 6
  residues processed: 28
  average time/residue: 0.0402
  time to fit residues: 1.7617
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0010
   chunk 57 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.5392

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.070195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.050332 restraints weight = 21282.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.09
r_work: 0.2876 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6548  Z= 0.242
  Angle     :  0.547   9.767   9217  Z= 0.298
  Chirality :  0.040   0.229   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.802 156.061   1792
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 23.85 %
    Favored  : 73.15 %
  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: -0.13 (0.36), residues: 552
  helix:  2.04 (0.38), residues: 167
  sheet: -0.24 (0.55), residues: 86
  loop : -1.34 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.013   0.002   TYR A 195 
 PHE   0.017   0.002   PHE B 124 
 TRP   0.010   0.002   TRP A 352 
 HIS   0.008   0.002   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.24 ( 6546)
  covalent geometry    : angle       0.54633 /  0.30 ( 9213)
  SS BOND              : bond        0.00516 /  0.31 (    2)
  SS BOND              : angle       1.14892 /  0.59 (    4)
  hydrogen bonds       : bond        0.06131 /  4.09 (  239)
  hydrogen bonds       : angle       4.28885 /  3.01 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 21
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8593 (mpp) cc_final: 0.8231 (mmm)
REVERT: A  229 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8327 (t70)
REVERT: A  258 TRP cc_start: 0.8263 (t60) cc_final: 0.7726 (t60)
REVERT: B  126 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8108 (tp-100)
  outliers start: 15
  outliers final: 9
  residues processed: 34
  average time/residue: 0.0520
  time to fit residues: 2.5199
Evaluate side-chains
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 21
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.070893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.051021 restraints weight = 21114.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 3.10
r_work: 0.2896 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6548  Z= 0.167
  Angle     :  0.492   9.080   9217  Z= 0.272
  Chirality :  0.038   0.219   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.781 156.243   1792
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 24.25 %
    Favored  : 73.55 %
  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 (0.36), residues: 552
  helix:  2.16 (0.38), residues: 167
  sheet: -0.19 (0.56), residues: 84
  loop : -1.34 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.012   0.001   TYR A 216 
 PHE   0.016   0.001   PHE B 320 
 TRP   0.011   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 ( 6546)
  covalent geometry    : angle       0.49150 /  0.27 ( 9213)
  SS BOND              : bond        0.00484 /  0.29 (    2)
  SS BOND              : angle       1.12484 /  0.57 (    4)
  hydrogen bonds       : bond        0.05696 /  3.82 (  239)
  hydrogen bonds       : angle       4.09932 /  2.87 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 21
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8614 (mpp) cc_final: 0.8248 (mmm)
REVERT: A  229 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8328 (t70)
REVERT: A  258 TRP cc_start: 0.8245 (t60) cc_final: 0.7724 (t60)
REVERT: B  126 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8019 (tp-100)
  outliers start: 11
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0513
  time to fit residues: 2.2448
Evaluate side-chains
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 21
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.070990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.051151 restraints weight = 21312.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 3.11
r_work: 0.2900 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6548  Z= 0.165
  Angle     :  0.484   7.959   9217  Z= 0.268
  Chirality :  0.038   0.200   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.779 156.532   1792
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 24.25 %
    Favored  : 73.55 %
  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:  0.00 (0.36), residues: 552
  helix:  2.18 (0.38), residues: 167
  sheet: -0.19 (0.56), residues: 86
  loop : -1.27 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.013   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 124 
 TRP   0.011   0.001   TRP A 352 
 HIS   0.005   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 6546)
  covalent geometry    : angle       0.48374 /  0.27 ( 9213)
  SS BOND              : bond        0.00482 /  0.29 (    2)
  SS BOND              : angle       1.05391 /  0.53 (    4)
  hydrogen bonds       : bond        0.05579 /  3.75 (  239)
  hydrogen bonds       : angle       4.03953 /  2.83 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 21
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8643 (mpp) cc_final: 0.8266 (mmm)
REVERT: A  229 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8321 (t70)
REVERT: A  258 TRP cc_start: 0.8249 (t60) cc_final: 0.7749 (t60)
REVERT: B  126 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8009 (tp-100)
  outliers start: 11
  outliers final: 9
  residues processed: 31
  average time/residue: 0.0511
  time to fit residues: 2.3461
Evaluate side-chains
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 21
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   88 THR
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 49 optimal weight:    0.0570
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.072305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.052527 restraints weight = 21128.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 3.09
r_work: 0.2943 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6548  Z= 0.100
  Angle     :  0.447   7.304   9217  Z= 0.248
  Chirality :  0.036   0.187   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.754 156.086   1792
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 24.85 %
    Favored  : 73.55 %
  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:  0.14 (0.36), residues: 552
  helix:  2.29 (0.38), residues: 167
  sheet: -0.02 (0.55), residues: 91
  loop : -1.23 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.006   0.001   TYR A 197 
 PHE   0.019   0.001   PHE B 320 
 TRP   0.011   0.001   TRP A 352 
 HIS   0.005   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.10 ( 6546)
  covalent geometry    : angle       0.44674 /  0.25 ( 9213)
  SS BOND              : bond        0.00405 /  0.24 (    2)
  SS BOND              : angle       0.86216 /  0.42 (    4)
  hydrogen bonds       : bond        0.04940 /  3.34 (  239)
  hydrogen bonds       : angle       3.79898 /  2.66 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8615 (mpp) cc_final: 0.8243 (mmm)
REVERT: A  229 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8330 (t70)
REVERT: A  258 TRP cc_start: 0.8195 (t60) cc_final: 0.7706 (t60)
REVERT: A  282 MET cc_start: 0.7979 (mtm) cc_final: 0.7647 (mtt)
REVERT: A  295 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8227 (tttp)
REVERT: B  126 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7877 (tp-100)
  outliers start: 8
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0612
  time to fit residues: 2.4261
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0370
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.2062

-------------------------------------------------------------------------------
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 = 0.3556 r_free = 0.3556 target = 0.071810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.051973 restraints weight = 21187.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.09
r_work: 0.2925 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6548  Z= 0.133
  Angle     :  0.453   6.917   9217  Z= 0.252
  Chirality :  0.037   0.188   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.762 156.261   1792
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 24.85 %
    Favored  : 73.55 %
  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:  0.11 (0.36), residues: 552
  helix:  2.25 (0.38), residues: 167
  sheet: -0.09 (0.55), residues: 91
  loop : -1.22 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.006   0.001   TYR A 195 
 PHE   0.017   0.001   PHE B 124 
 TRP   0.011   0.001   TRP A 352 
 HIS   0.004   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 6546)
  covalent geometry    : angle       0.45272 /  0.25 ( 9213)
  SS BOND              : bond        0.00458 /  0.27 (    2)
  SS BOND              : angle       0.84687 /  0.42 (    4)
  hydrogen bonds       : bond        0.05100 /  3.43 (  239)
  hydrogen bonds       : angle       3.86294 /  2.70 (  618)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8642 (mpp) cc_final: 0.8263 (mmm)
REVERT: A  229 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8369 (t70)
REVERT: A  258 TRP cc_start: 0.8198 (t60) cc_final: 0.7729 (t60)
REVERT: B  126 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7976 (tp-100)
  outliers start: 8
  outliers final: 6
  residues processed: 28
  average time/residue: 0.0583
  time to fit residues: 2.4330
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASP
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  295 LYS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0050
   chunk 20 optimal weight:    0.0070
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4812

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.072971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.053197 restraints weight = 21062.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.09
r_work: 0.2961 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6548  Z= 0.093
  Angle     :  0.431   6.204   9217  Z= 0.240
  Chirality :  0.036   0.183   1063
  Planarity :  0.003   0.035    907
  Dihedral  : 20.732 155.858   1792
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 24.65 %
    Favored  : 73.55 %
  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:  0.21 (0.35), residues: 552
  helix:  2.33 (0.38), residues: 167
  sheet:  0.02 (0.55), residues: 91
  loop : -1.18 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 280 
 TYR   0.006   0.001   TYR A 197 
 PHE   0.020   0.001   PHE B 320 
 TRP   0.010   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.09 ( 6546)
  covalent geometry    : angle       0.43046 /  0.24 ( 9213)
  SS BOND              : bond        0.00326 /  0.19 (    2)
  SS BOND              : angle       0.75689 /  0.37 (    4)
  hydrogen bonds       : bond        0.04653 /  3.15 (  239)
  hydrogen bonds       : angle       3.69677 /  2.59 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1074.67 seconds
wall clock time: 19 minutes 8.41 seconds (1148.41 seconds total)