Starting phenix.real_space_refine
on Sat May 10 12:19:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enc_19831/05_2025/9enc_19831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enc_19831/05_2025/9enc_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_19831/05_2025/9enc_19831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enc_19831/05_2025/9enc_19831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enc_19831/05_2025/9enc_19831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enc_19831/05_2025/9enc_19831.cif"
  }
  resolution = 3.36
  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=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.88, per 1000 atoms: 0.78
  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: 1.57
  Conformation dependent library (CDL) restraints added in 662.6 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: 1.75
  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: 1.75

  Time building geometry restraints manager: 1.85 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=" 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=" 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
  angle pdb=" C4'   G D  36 "
        pdb=" C3'   G D  36 "
        pdb=" O3'   G D  36 "
      ideal   model   delta    sigma   weight residual
     109.40  113.35   -3.95 1.50e+00 4.44e-01 6.93e+00
  angle pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
        pdb=" N   PRO A 321 "
      ideal   model   delta    sigma   weight residual
     118.44  122.46   -4.02 1.59e+00 3.96e-01 6.39e+00
  angle pdb=" N   PHE A 320 "
        pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
      ideal   model   delta    sigma   weight residual
     109.81  114.97   -5.16 2.21e+00 2.05e-01 5.44e+00
  ... (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:             1.720
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.260
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
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= 0.122
  Angle     :  0.512  10.339   9217  Z= 0.292
  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 (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: -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
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS B 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 216 
 ARG   0.003   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19239 (  239)
  hydrogen bonds       : angle       6.40376 (  618)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       0.66776 (    4)
  covalent geometry    : bond        0.00234 ( 6546)
  covalent geometry    : angle       0.51214 ( 9213)

*********************** 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  : 0.614 
Fit side-chains
REVERT: A  293 MET cc_start: 0.7799 (ttt) cc_final: 0.7592 (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: 0.2628
  time to fit residues: 11.3285
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  : 0.548 
-------------------------------------------------------------------------------
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 53 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.072373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.053141 restraints weight = 20555.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 3.04
r_work: 0.2962 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1151

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= 0.151
  Angle     :  0.527  10.950   9217  Z= 0.275
  Chirality :  0.038   0.241   1063
  Planarity :  0.004   0.032    907
  Dihedral  : 20.786 154.016   1796
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 25.85 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.20 (0.36), residues: 552
  helix:  2.07 (0.38), residues: 167
  sheet:  0.47 (0.58), residues: 84
  loop : -1.15 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 258 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.003   0.001   ARG A 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05232 (  239)
  hydrogen bonds       : angle       4.25883 (  618)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       0.86119 (    4)
  covalent geometry    : bond        0.00335 ( 6546)
  covalent geometry    : angle       0.52657 ( 9213)

*********************** 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
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8479 (mpp) cc_final: 0.8138 (mmm)
REVERT: A  258 TRP cc_start: 0.8126 (t60) cc_final: 0.7506 (t60)
REVERT: A  293 MET cc_start: 0.7780 (ttt) cc_final: 0.7577 (ttm)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1776
  time to fit residues: 7.2065
Evaluate side-chains
  23 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 59 optimal weight:   10.0000
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3613 r_free = 0.3613 target = 0.074099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054590 restraints weight = 20915.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.10
r_work: 0.3009 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1559

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= 0.096
  Angle     :  0.470   9.360   9217  Z= 0.244
  Chirality :  0.036   0.217   1063
  Planarity :  0.003   0.031    907
  Dihedral  : 20.688 153.928   1796
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.05 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.51 (0.36), residues: 552
  helix:  2.53 (0.38), residues: 167
  sheet:  0.55 (0.57), residues: 91
  loop : -1.10 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE B 320 
 TYR   0.008   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04244 (  239)
  hydrogen bonds       : angle       3.69806 (  618)
  SS BOND              : bond        0.00290 (    2)
  SS BOND              : angle       0.58863 (    4)
  covalent geometry    : bond        0.00200 ( 6546)
  covalent geometry    : angle       0.47041 ( 9213)

*********************** 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
  33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8505 (mpp) cc_final: 0.8126 (mmm)
REVERT: A  258 TRP cc_start: 0.8047 (t60) cc_final: 0.7526 (t60)
REVERT: A  293 MET cc_start: 0.7650 (ttt) cc_final: 0.7312 (ttm)
REVERT: B   72 MET cc_start: 0.8509 (mmm) cc_final: 0.7705 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1614
  time to fit residues: 7.0161
Evaluate side-chains
  24 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  295 LYS
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 12 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0570
   overall best weight:    1.0702

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.072856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.053074 restraints weight = 20998.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 3.09
r_work: 0.2969 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1699

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= 0.129
  Angle     :  0.485   6.993   9217  Z= 0.252
  Chirality :  0.036   0.180   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.745 155.601   1796
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.65 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.36), residues: 552
  helix:  2.51 (0.38), residues: 167
  sheet:  0.43 (0.56), residues: 91
  loop : -1.10 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.015   0.001   PHE B 124 
 TYR   0.010   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  239)
  hydrogen bonds       : angle       3.77325 (  618)
  SS BOND              : bond        0.00414 (    2)
  SS BOND              : angle       0.85565 (    4)
  covalent geometry    : bond        0.00287 ( 6546)
  covalent geometry    : angle       0.48487 ( 9213)

*********************** 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
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8588 (mpp) cc_final: 0.8199 (mmm)
REVERT: A  229 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8106 (t0)
REVERT: A  258 TRP cc_start: 0.8154 (t60) cc_final: 0.7704 (t60)
REVERT: A  293 MET cc_start: 0.7760 (ttt) cc_final: 0.7389 (ttm)
  outliers start: 9
  outliers final: 5
  residues processed: 29
  average time/residue: 0.1985
  time to fit residues: 7.9846
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  133 ARG
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 29 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.070663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.050901 restraints weight = 21101.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 3.07
r_work: 0.2906 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1937

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= 0.244
  Angle     :  0.578   6.396   9217  Z= 0.296
  Chirality :  0.039   0.189   1063
  Planarity :  0.004   0.032    907
  Dihedral  : 20.915 158.693   1792
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.25 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.13 (0.36), residues: 552
  helix:  2.23 (0.38), residues: 167
  sheet:  0.02 (0.55), residues: 91
  loop : -1.22 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  74 
 HIS   0.006   0.002   HIS B 360 
 PHE   0.018   0.002   PHE B  94 
 TYR   0.014   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05790 (  239)
  hydrogen bonds       : angle       4.13061 (  618)
  SS BOND              : bond        0.00493 (    2)
  SS BOND              : angle       1.21321 (    4)
  covalent geometry    : bond        0.00555 ( 6546)
  covalent geometry    : angle       0.57745 ( 9213)

*********************** 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
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8648 (mpp) cc_final: 0.8261 (mmm)
REVERT: A  229 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8316 (t70)
REVERT: A  258 TRP cc_start: 0.8226 (t60) cc_final: 0.7728 (t60)
REVERT: A  293 MET cc_start: 0.7819 (ttt) cc_final: 0.7396 (ttm)
  outliers start: 8
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1630
  time to fit residues: 6.7649
Evaluate side-chains
  26 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue  133 ARG
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 19 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 21 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.072212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.052294 restraints weight = 20794.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 3.10
r_work: 0.2935 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6548  Z= 0.131
  Angle     :  0.480   5.923   9217  Z= 0.249
  Chirality :  0.036   0.182   1063
  Planarity :  0.003   0.033    907
  Dihedral  : 20.893 158.624   1792
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.45 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.29 (0.36), residues: 552
  helix:  2.44 (0.38), residues: 167
  sheet:  0.11 (0.56), residues: 91
  loop : -1.18 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.007   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04748 (  239)
  hydrogen bonds       : angle       3.79159 (  618)
  SS BOND              : bond        0.00406 (    2)
  SS BOND              : angle       0.83919 (    4)
  covalent geometry    : bond        0.00290 ( 6546)
  covalent geometry    : angle       0.47936 ( 9213)

*********************** 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
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8696 (mpp) cc_final: 0.8286 (mmm)
REVERT: A  229 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8351 (t70)
REVERT: A  258 TRP cc_start: 0.8211 (t60) cc_final: 0.7752 (t60)
REVERT: A  293 MET cc_start: 0.7801 (ttt) cc_final: 0.7415 (ttm)
  outliers start: 8
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1617
  time to fit residues: 6.8171
Evaluate side-chains
  26 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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  323 VAL
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 19 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.071783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.051788 restraints weight = 21044.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 3.11
r_work: 0.2921 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2133

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     :  0.497   6.035   9217  Z= 0.256
  Chirality :  0.036   0.186   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 20.968 159.479   1792
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.45 %
    Favored  : 74.75 %
  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:  0.23 (0.36), residues: 552
  helix:  2.36 (0.38), residues: 167
  sheet:  0.04 (0.56), residues: 89
  loop : -1.16 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.016   0.001   PHE B 124 
 TYR   0.008   0.001   TYR A 195 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05024 (  239)
  hydrogen bonds       : angle       3.83888 (  618)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       0.97131 (    4)
  covalent geometry    : bond        0.00346 ( 6546)
  covalent geometry    : angle       0.49679 ( 9213)

*********************** 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
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8734 (mpp) cc_final: 0.8327 (mmm)
REVERT: A  229 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8316 (t70)
REVERT: A  258 TRP cc_start: 0.8256 (t60) cc_final: 0.7817 (t60)
REVERT: A  293 MET cc_start: 0.7805 (ttt) cc_final: 0.7406 (ttm)
REVERT: B  126 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8009 (tp-100)
  outliers start: 9
  outliers final: 6
  residues processed: 29
  average time/residue: 0.1450
  time to fit residues: 7.0661
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  : 0.598 
-------------------------------------------------------------------------------
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  287 PHE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  126 GLN
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 52 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0040
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.4000

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.068321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.048405 restraints weight = 20941.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.21
r_work: 0.2781 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6548  Z= 0.240
  Angle     :  0.559   5.880   9217  Z= 0.289
  Chirality :  0.039   0.201   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 21.149 166.678   1792
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  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 (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: -0.04 (0.36), residues: 552
  helix:  2.09 (0.38), residues: 167
  sheet: -0.27 (0.55), residues: 90
  loop : -1.25 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  74 
 HIS   0.006   0.001   HIS B 360 
 PHE   0.017   0.002   PHE B 124 
 TYR   0.012   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05940 (  239)
  hydrogen bonds       : angle       4.10270 (  618)
  SS BOND              : bond        0.00504 (    2)
  SS BOND              : angle       1.24281 (    4)
  covalent geometry    : bond        0.00547 ( 6546)
  covalent geometry    : angle       0.55901 ( 9213)

*********************** 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
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8795 (mpp) cc_final: 0.8348 (mmm)
REVERT: A  229 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8154 (t0)
REVERT: A  258 TRP cc_start: 0.8391 (t60) cc_final: 0.7927 (t60)
REVERT: A  293 MET cc_start: 0.7814 (ttt) cc_final: 0.7332 (ttm)
REVERT: B  126 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7974 (tp-100)
REVERT: B  228 MET cc_start: 0.8882 (ppp) cc_final: 0.8602 (ppp)
  outliers start: 8
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1359
  time to fit residues: 6.5020
Evaluate side-chains
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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 B residue  126 GLN
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 23 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.072781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.052854 restraints weight = 20944.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 3.10
r_work: 0.2953 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6548  Z= 0.110
  Angle     :  0.466   5.858   9217  Z= 0.240
  Chirality :  0.035   0.184   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 21.051 166.432   1792
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 24.25 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.25 (0.36), residues: 552
  helix:  2.41 (0.38), residues: 167
  sheet:  0.04 (0.57), residues: 89
  loop : -1.18 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.021   0.001   PHE B 320 
 TYR   0.010   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04595 (  239)
  hydrogen bonds       : angle       3.70205 (  618)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.68308 (    4)
  covalent geometry    : bond        0.00239 ( 6546)
  covalent geometry    : angle       0.46598 ( 9213)

*********************** 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
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8701 (mpp) cc_final: 0.8299 (mmm)
REVERT: A  229 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8318 (t70)
REVERT: A  258 TRP cc_start: 0.8177 (t60) cc_final: 0.7744 (t60)
REVERT: A  293 MET cc_start: 0.7808 (ttt) cc_final: 0.7401 (ttm)
REVERT: B  126 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7954 (tp-100)
REVERT: B  228 MET cc_start: 0.8765 (ppp) cc_final: 0.8536 (ppp)
  outliers start: 6
  outliers final: 3
  residues processed: 27
  average time/residue: 0.1324
  time to fit residues: 5.7857
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  126 GLN
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 53 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0000
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.4604

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.074871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.054894 restraints weight = 21069.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 3.09
r_work: 0.3008 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6548  Z= 0.088
  Angle     :  0.432   5.938   9217  Z= 0.223
  Chirality :  0.034   0.155   1063
  Planarity :  0.003   0.037    907
  Dihedral  : 20.964 165.241   1792
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.85 %
    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 (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:  0.45 (0.36), residues: 552
  helix:  2.63 (0.38), residues: 169
  sheet:  0.26 (0.58), residues: 88
  loop : -1.16 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 355 
 PHE   0.023   0.001   PHE B 320 
 TYR   0.010   0.001   TYR A 216 
 ARG   0.003   0.000   ARG B 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  239)
  hydrogen bonds       : angle       3.42824 (  618)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       0.51156 (    4)
  covalent geometry    : bond        0.00187 ( 6546)
  covalent geometry    : angle       0.43224 ( 9213)

********************** 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
  28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8724 (mpp) cc_final: 0.8293 (mmm)
REVERT: A  229 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8139 (t0)
REVERT: A  258 TRP cc_start: 0.8118 (t60) cc_final: 0.7729 (t60)
REVERT: A  293 MET cc_start: 0.7755 (ttt) cc_final: 0.7455 (ttm)
REVERT: B  126 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7911 (tp-100)
  outliers start: 5
  outliers final: 3
  residues processed: 27
  average time/residue: 0.1398
  time to fit residues: 6.3242
Evaluate side-chains
  27 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue  126 GLN
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 27 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.069323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.049135 restraints weight = 21447.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 3.25
r_work: 0.2791 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6548  Z= 0.221
  Angle     :  0.537   5.992   9217  Z= 0.275
  Chirality :  0.038   0.186   1063
  Planarity :  0.004   0.037    907
  Dihedral  : 21.135 168.470   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 23.85 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.13 (0.36), residues: 552
  helix:  2.25 (0.38), residues: 167
  sheet: -0.01 (0.56), residues: 89
  loop : -1.23 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.025   0.002   PHE B 320 
 TYR   0.012   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05553 (  239)
  hydrogen bonds       : angle       3.94537 (  618)
  SS BOND              : bond        0.00508 (    2)
  SS BOND              : angle       1.17127 (    4)
  covalent geometry    : bond        0.00503 ( 6546)
  covalent geometry    : angle       0.53647 ( 9213)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2820.51 seconds
wall clock time: 49 minutes 47.23 seconds (2987.23 seconds total)