Starting phenix.real_space_refine
on Tue Mar 11 15:32:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enc_19831/03_2025/9enc_19831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enc_19831/03_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_19831/03_2025/9enc_19831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enc_19831/03_2025/9enc_19831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enc_19831/03_2025/9enc_19831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enc_19831/03_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-5624/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: 4.89, 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: 1.74
  Conformation dependent library (CDL) restraints added in 726.2 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: 2.24
  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: 1.89

  Time building geometry restraints manager: 2.04 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:             1.470
  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:                     21.340
  Find NCS groups from input model:        0.210
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.320
-------------------------------------------------------------------------------
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   6546  Z= 0.153
  Angle     :  0.512  10.339   9213  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 

*********************** 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: 0.2548
  time to fit residues: 10.9527
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  : 0.609 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.053142 restraints weight = 20555.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.04
r_work: 0.2962 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
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   6546  Z= 0.217
  Angle     :  0.527  10.950   9213  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 

*********************** 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  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8477 (mpp) cc_final: 0.8137 (mmm)
REVERT: A  258 TRP cc_start: 0.8129 (t60) cc_final: 0.7508 (t60)
REVERT: A  293 MET cc_start: 0.7782 (ttt) cc_final: 0.7578 (ttm)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1810
  time to fit residues: 7.4638
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  : 0.617 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0980
   chunk 21 optimal weight:    0.0770
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0070
   chunk 8 optimal weight:    0.8980
   chunk 59 optimal weight:    9.9990
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.074816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.055311 restraints weight = 20903.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 3.09
r_work: 0.3029 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6546  Z= 0.119
  Angle     :  0.466   9.401   9213  Z= 0.242
  Chirality :  0.035   0.218   1063
  Planarity :  0.003   0.031    907
  Dihedral  : 20.675 153.557   1796
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 24.25 %
    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:  0.52 (0.36), residues: 552
  helix:  2.50 (0.38), residues: 169
  sheet:  0.55 (0.58), residues: 90
  loop : -1.08 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.019   0.001   PHE B 320 
 TYR   0.008   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 193 

*********************** 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
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8469 (mpp) cc_final: 0.8082 (mmm)
REVERT: A  258 TRP cc_start: 0.8011 (t60) cc_final: 0.7474 (t60)
REVERT: B   72 MET cc_start: 0.8450 (mmm) cc_final: 0.7738 (mmm)
  outliers start: 9
  outliers final: 3
  residues processed: 29
  average time/residue: 0.1551
  time to fit residues: 6.9158
Evaluate side-chains
  25 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 PHE
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:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.071679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.051918 restraints weight = 21076.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.08
r_work: 0.2936 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6546  Z= 0.279
  Angle     :  0.534   7.257   9213  Z= 0.277
  Chirality :  0.038   0.181   1063
  Planarity :  0.004   0.035    907
  Dihedral  : 20.792 156.289   1796
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.85 %
    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:  0.33 (0.36), residues: 552
  helix:  2.38 (0.38), residues: 167
  sheet:  0.26 (0.55), residues: 93
  loop : -1.15 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.017   0.002   PHE B  94 
 TYR   0.012   0.001   TYR B 216 
 ARG   0.003   0.000   ARG A 201 

*********************** 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
  32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8593 (mpp) cc_final: 0.8218 (mmm)
REVERT: A  229 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8147 (t0)
REVERT: A  258 TRP cc_start: 0.8217 (t60) cc_final: 0.7776 (t60)
  outliers start: 10
  outliers final: 4
  residues processed: 29
  average time/residue: 0.2001
  time to fit residues: 8.1350
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  : 0.581 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.070971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.051266 restraints weight = 21073.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.06
r_work: 0.2919 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6546  Z= 0.295
  Angle     :  0.539   6.180   9213  Z= 0.278
  Chirality :  0.038   0.192   1063
  Planarity :  0.004   0.033    907
  Dihedral  : 20.932 159.100   1792
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 24.25 %
    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:  0.16 (0.36), residues: 552
  helix:  2.28 (0.38), residues: 167
  sheet:  0.08 (0.55), residues: 91
  loop : -1.24 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.016   0.002   PHE B 124 
 TYR   0.010   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 159 

*********************** 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: 7
    poor density    : 22
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8617 (mpp) cc_final: 0.8238 (mmm)
REVERT: A  229 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8323 (t70)
REVERT: A  258 TRP cc_start: 0.8218 (t60) cc_final: 0.7738 (t60)
  outliers start: 7
  outliers final: 5
  residues processed: 28
  average time/residue: 0.1699
  time to fit residues: 7.0557
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  : 0.590 
-------------------------------------------------------------------------------
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   74 TRP
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:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.070771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.050886 restraints weight = 20946.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 3.08
r_work: 0.2893 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6546  Z= 0.302
  Angle     :  0.541   5.976   9213  Z= 0.280
  Chirality :  0.038   0.197   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.002 159.695   1792
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.85 %
    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:  0.08 (0.36), residues: 552
  helix:  2.22 (0.38), residues: 167
  sheet: -0.12 (0.54), residues: 93
  loop : -1.25 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  74 
 HIS   0.006   0.001   HIS B 360 
 PHE   0.016   0.002   PHE B 124 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.003   0.000   ARG A 201 

*********************** 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
  30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8718 (mpp) cc_final: 0.8317 (mmm)
REVERT: A  229 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8310 (t70)
REVERT: A  258 TRP cc_start: 0.8261 (t60) cc_final: 0.7822 (t60)
  outliers start: 9
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1624
  time to fit residues: 7.0367
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  : 0.576 
-------------------------------------------------------------------------------
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 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 19 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.4388

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.071754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.051931 restraints weight = 21109.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.09
r_work: 0.2923 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6546  Z= 0.229
  Angle     :  0.502   6.170   9213  Z= 0.258
  Chirality :  0.037   0.194   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.016 164.944   1792
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.13
  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:  0.16 (0.36), residues: 552
  helix:  2.36 (0.38), residues: 167
  sheet: -0.07 (0.57), residues: 89
  loop : -1.23 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   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 A 195 
 ARG   0.001   0.000   ARG A 201 

*********************** 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
  31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8704 (mpp) cc_final: 0.8296 (mmm)
REVERT: A  229 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8316 (t70)
REVERT: A  258 TRP cc_start: 0.8202 (t60) cc_final: 0.7763 (t60)
REVERT: B  126 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8026 (tp-100)
  outliers start: 9
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1726
  time to fit residues: 7.4240
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  : 0.577 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.068535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.048591 restraints weight = 21133.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 3.22
r_work: 0.2782 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6546  Z= 0.327
  Angle     :  0.547   5.944   9213  Z= 0.282
  Chirality :  0.038   0.201   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.146 167.474   1792
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.05 %
    Favored  : 75.55 %
  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: -0.05 (0.36), residues: 552
  helix:  2.17 (0.38), residues: 167
  sheet: -0.29 (0.55), residues: 91
  loop : -1.31 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  74 
 HIS   0.006   0.001   HIS B 360 
 PHE   0.020   0.002   PHE B 320 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.002   0.000   ARG A 201 

*********************** 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
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8811 (mpp) cc_final: 0.8358 (mmm)
REVERT: A  229 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8127 (t0)
REVERT: A  258 TRP cc_start: 0.8364 (t60) cc_final: 0.7876 (t60)
REVERT: B  126 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8092 (tp-100)
REVERT: B  228 MET cc_start: 0.8888 (ppp) cc_final: 0.8663 (ppp)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.1414
  time to fit residues: 6.2504
Evaluate side-chains
  29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  316 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.071119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.051093 restraints weight = 21204.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 3.26
r_work: 0.2849 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6546  Z= 0.148
  Angle     :  0.459   5.855   9213  Z= 0.236
  Chirality :  0.035   0.183   1063
  Planarity :  0.003   0.034    907
  Dihedral  : 21.054 167.099   1792
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 23.65 %
    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:  0.27 (0.36), residues: 552
  helix:  2.50 (0.38), residues: 167
  sheet:  0.05 (0.58), residues: 89
  loop : -1.22 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.021   0.001   PHE B 320 
 TYR   0.005   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 280 

*********************** 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  : 0.609 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8755 (mpp) cc_final: 0.8281 (mmm)
REVERT: A  229 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8312 (t70)
REVERT: A  258 TRP cc_start: 0.8272 (t60) cc_final: 0.7776 (t60)
  outliers start: 6
  outliers final: 3
  residues processed: 26
  average time/residue: 0.1366
  time to fit residues: 5.7783
Evaluate side-chains
  26 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  316 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0070
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.070602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.050565 restraints weight = 21288.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 3.25
r_work: 0.2834 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6546  Z= 0.171
  Angle     :  0.461   5.871   9213  Z= 0.238
  Chirality :  0.035   0.178   1063
  Planarity :  0.003   0.035    907
  Dihedral  : 21.071 167.611   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 23.65 %
    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:  0.29 (0.36), residues: 552
  helix:  2.52 (0.38), residues: 167
  sheet:  0.06 (0.58), residues: 89
  loop : -1.21 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.023   0.001   PHE B 320 
 TYR   0.006   0.001   TYR A 197 
 ARG   0.001   0.000   ARG B 196 

********************** 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: 6
    poor density    : 22
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8806 (mpp) cc_final: 0.8336 (mmm)
REVERT: A  229 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8306 (t70)
REVERT: A  258 TRP cc_start: 0.8281 (t60) cc_final: 0.7784 (t60)
  outliers start: 6
  outliers final: 4
  residues processed: 26
  average time/residue: 0.1311
  time to fit residues: 5.5551
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  : 0.573 
-------------------------------------------------------------------------------
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 B residue  167 VAL
Chi-restraints excluded: chain B residue  316 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.069561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.049491 restraints weight = 21310.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.23
r_work: 0.2806 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6546  Z= 0.255
  Angle     :  0.503   5.946   9213  Z= 0.259
  Chirality :  0.037   0.186   1063
  Planarity :  0.004   0.034    907
  Dihedral  : 21.157 169.182   1792
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  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:  0.12 (0.36), residues: 552
  helix:  2.35 (0.38), residues: 167
  sheet: -0.08 (0.57), residues: 89
  loop : -1.28 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 360 
 PHE   0.021   0.002   PHE B 320 
 TYR   0.009   0.001   TYR A 195 
 ARG   0.002   0.000   ARG B 196 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2933.09 seconds
wall clock time: 51 minutes 1.17 seconds (3061.17 seconds total)