Starting phenix.real_space_refine
on Wed Aug  5 02:02:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enb_19830/08_2026/9enb_19830.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     142      5.49       5
     Mg      6      5.21       5
     S      34      5.16       5
     C    4700      2.51       5
     N    1440      2.21       5
     O    1942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8264
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2602
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 14, 'TRANS': 303}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2602
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 14, 'TRANS': 303}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1527
          Classifications: {'RNA': 72}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 12, 'rna3p': 59}
    Chain: "D"
      Number of atoms: 1527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1527
          Classifications: {'RNA': 72}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 12, 'rna3p': 59}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.01, per 1000 atoms: 0.24
  Number of scatterers: 8264
  At special positions: 0
  Unit cell: (104.009, 131.068, 68.4936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     P     142     15.00
     Mg      6     11.99
     O    1942      8.00
     N    1440      7.00
     C    4700      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=2.04
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 327 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 270.1 milliseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1208

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      36.6% alpha, 24.2% beta
      45 base pairs and 66 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 60
      removed outlier: 3.725A  pdb=" N   ALA A  59 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   HIS A  60 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 56 through 60'
    Processing helix  chain 'A' and resid 72 through 76
      removed outlier: 4.442A  pdb=" N   GLY A  75 " --> pdb=" O   MET A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 100
      removed outlier: 3.514A  pdb=" N   LYS A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
      removed outlier: 3.531A  pdb=" N   SER A 109 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 4.059A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 223 through 226
      removed outlier: 4.248A  pdb=" N   CYS A 226 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 223 through 226'
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.536A  pdb=" N   LEU A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 303
      removed outlier: 3.577A  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 56 through 60
      removed outlier: 3.723A  pdb=" N   ALA B  59 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   HIS B  60 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 60'
    Processing helix  chain 'B' and resid 72 through 76
      removed outlier: 4.425A  pdb=" N   GLY B  75 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.564A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 3.501A  pdb=" N   THR B 108 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 168
      removed outlier: 4.046A  pdb=" N   VAL B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.553A  pdb=" N   GLN B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 4.206A  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 229 through 233
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.534A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.526A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
    Processing helix  chain 'B' and resid 413 through 417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 5.269A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY A  61 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   HIS A  64 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ALA A  66 " --> pdb=" O   TRP A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.678A  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: 6.426A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 8.924A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 10.976A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU A 264 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.630A  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: 5.349A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.677A  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: 6.447A  pdb=" N   ASP B 326 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   GLN B 126 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   LYS B 328 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
      removed outlier: 10.960A  pdb=" N   ILE B 128 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LEU B 264 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN B 266 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   VAL B 246 " --> pdb=" O   GLN B 266 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA B 244 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG B 239 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      118 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      45 basepair parallelities
      66 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1876
        1.33 -     1.45: 2667
        1.45 -     1.57: 3859
        1.57 -     1.69: 284
        1.69 -     1.81: 54
  Bond restraints: 8740
  Sorted by residual:
  bond pdb=" N1    C D  27 "
       pdb=" C6    C D  27 "
    ideal  model  delta    sigma   weight residual
    1.367  1.356  0.011 6.00e-03 2.78e+04 3.66e+00
  bond pdb=" N1    C C  27 "
       pdb=" C6    C C  27 "
    ideal  model  delta    sigma   weight residual
    1.367  1.356  0.011 6.00e-03 2.78e+04 3.63e+00
  bond pdb=" C5    G C  29 "
       pdb=" C4    G C  29 "
    ideal  model  delta    sigma   weight residual
    1.379  1.366  0.013 7.00e-03 2.04e+04 3.28e+00
  bond pdb=" C5    G D  29 "
       pdb=" C4    G D  29 "
    ideal  model  delta    sigma   weight residual
    1.379  1.367  0.012 7.00e-03 2.04e+04 2.82e+00
  bond pdb=" N7    A C  58 "
       pdb=" C5    A C  58 "
    ideal  model  delta    sigma   weight residual
    1.388  1.378  0.010 6.00e-03 2.78e+04 2.80e+00
  ... (remaining 8735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 11637
        1.23 -     2.46: 579
        2.46 -     3.69: 272
        3.69 -     4.92: 18
        4.92 -     6.15: 4
  Bond angle restraints: 12510
  Sorted by residual:
  angle pdb=" C1'   C C  48 "
        pdb=" N1    C C  48 "
        pdb=" C2    C C  48 "
      ideal   model   delta    sigma   weight residual
     118.80  124.64   -5.84 1.10e+00 8.26e-01 2.82e+01
  angle pdb=" C1'   C D  48 "
        pdb=" N1    C D  48 "
        pdb=" C2    C D  48 "
      ideal   model   delta    sigma   weight residual
     118.80  124.62   -5.82 1.10e+00 8.26e-01 2.80e+01
  angle pdb=" N1    C C  48 "
        pdb=" C2    C C  48 "
        pdb=" O2    C C  48 "
      ideal   model   delta    sigma   weight residual
     118.90  121.84   -2.94 6.00e-01 2.78e+00 2.40e+01
  angle pdb=" N1    C D  48 "
        pdb=" C2    C D  48 "
        pdb=" O2    C D  48 "
      ideal   model   delta    sigma   weight residual
     118.90  121.81   -2.91 6.00e-01 2.78e+00 2.35e+01
  angle pdb=" O5'   U C  16 "
        pdb=" C5'   U C  16 "
        pdb=" C4'   U C  16 "
      ideal   model   delta    sigma   weight residual
     109.40  113.11   -3.71 8.00e-01 1.56e+00 2.15e+01
  ... (remaining 12505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 4977
       35.54 -    71.08: 401
       71.08 -   106.62: 56
      106.62 -   142.16: 3
      142.16 -   177.70: 5
  Dihedral angle restraints: 5442
    sinusoidal: 3578
      harmonic: 1864
  Sorted by residual:
  dihedral pdb=" O4'   C C  48 "
           pdb=" C1'   C C  48 "
           pdb=" N1    C C  48 "
           pdb=" C2    C C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -8.90 -151.10     1      1.50e+01 4.44e-03 8.00e+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   -9.07 -150.93     1      1.50e+01 4.44e-03 8.00e+01
  dihedral pdb=" O4'   U C  34 "
           pdb=" C1'   U C  34 "
           pdb=" N1    U C  34 "
           pdb=" C2    U C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.64 -176.64     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 5439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1090
       0.051 -    0.102: 235
       0.102 -    0.153: 153
       0.153 -    0.204: 2
       0.204 -    0.254: 2
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" C1'   A D  38 "
            pdb=" O4'   A D  38 "
            pdb=" C2'   A D  38 "
            pdb=" N9    A D  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.22    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C1'   U C  39 "
            pdb=" O4'   U C  39 "
            pdb=" C2'   U C  39 "
            pdb=" N1    U C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.23    0.24 2.00e-01 2.50e+01 1.42e+00
  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    2.33    0.18 2.00e-01 2.50e+01 7.97e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  38 "   -0.027 2.00e-02 2.50e+03   1.35e-02 5.03e+00
        pdb=" N9    A D  38 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A D  38 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  38 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  38 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  38 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A D  38 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  38 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  39 "    0.022 2.00e-02 2.50e+03   1.33e-02 3.97e+00
        pdb=" N1    U C  39 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    U C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U C  39 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    U C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U C  39 "    0.003 2.00e-02 2.50e+03
        pdb=" O4    U C  39 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U C  39 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U C  39 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 320 "   -0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO B 321 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 321 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 321 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1073 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 429
        2.70 -     3.25: 7178
        3.25 -     3.80: 14293
        3.80 -     4.35: 18866
        4.35 -     4.90: 28528
  Nonbonded interactions: 69294
  Sorted by model distance:
  nonbonded pdb=" OP2   G D   9 "
            pdb="MG    MG D 102 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" OP2   G C   9 "
            pdb="MG    MG C 102 "
     model   vdw
     2.162 2.170
  nonbonded pdb=" OE2 GLU B 294 "
            pdb=" OH  TYR B 411 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O2'   G C  36 "
            pdb=" OP2   A C  37 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OE2 GLU A 294 "
            pdb=" OH  TYR A 411 "
     model   vdw
     2.250 3.040
  ... (remaining 69289 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             2.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.090
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
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      :  0.006   0.042   8742  Z= 0.398
  Angle     :  0.709   6.147  12514  Z= 0.548
  Chirality :  0.056   0.254   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 22.369 177.702   4228
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 25.27 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.33), residues: 620
  helix:  0.93 (0.39), residues: 166
  sheet:  1.03 (0.56), residues: 82
  loop : -0.78 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 133 
 TYR   0.009   0.001   TYR A 216 
 PHE   0.016   0.001   PHE B 320 
 TRP   0.012   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00601 /  0.40 ( 8740)
  covalent geometry    : angle       0.70904 /  0.55 (12510)
  SS BOND              : bond        0.00888 /  0.44 (    2)
  SS BOND              : angle       1.17487 /  0.61 (    4)
  hydrogen bonds       : bond        0.17213 / 11.60 (  313)
  hydrogen bonds       : angle       5.56689 /  3.79 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.7892 (mt0) cc_final: 0.7497 (mt0)
REVERT: A  412 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7278 (ttpp)
REVERT: B   72 MET cc_start: 0.8292 (mmm) cc_final: 0.7783 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 30
  average time/residue: 0.5515
  time to fit residues: 17.6037
Evaluate side-chains
  28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.092163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.064000 restraints weight = 17678.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.17
r_work: 0.2899 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.0579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8742  Z= 0.162
  Angle     :  0.514   5.936  12514  Z= 0.294
  Chirality :  0.038   0.174   1482
  Planarity :  0.004   0.041   1076
  Dihedral  : 22.096 179.042   2954
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.22 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.33), residues: 620
  helix:  1.51 (0.39), residues: 166
  sheet:  1.65 (0.56), residues: 72
  loop : -0.66 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.007   0.001   TYR B 197 
 PHE   0.018   0.001   PHE B 320 
 TRP   0.007   0.001   TRP B  74 
 HIS   0.007   0.002   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8740)
  covalent geometry    : angle       0.51387 /  0.29 (12510)
  SS BOND              : bond        0.00729 /  0.37 (    2)
  SS BOND              : angle       1.03058 /  0.53 (    4)
  hydrogen bonds       : bond        0.06801 /  4.61 (  313)
  hydrogen bonds       : angle       4.10448 /  2.84 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8521 (mt0) cc_final: 0.7766 (mt0)
REVERT: A  412 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7099 (ttpp)
REVERT: B   72 MET cc_start: 0.8713 (mmm) cc_final: 0.8258 (mmm)
  outliers start: 14
  outliers final: 2
  residues processed: 36
  average time/residue: 0.4505
  time to fit residues: 17.4989
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  412 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 259 GLN
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.091964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.063726 restraints weight = 17580.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.17
r_work: 0.2892 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.0662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8742  Z= 0.188
  Angle     :  0.524   8.291  12514  Z= 0.294
  Chirality :  0.039   0.171   1482
  Planarity :  0.004   0.043   1076
  Dihedral  : 22.042 179.816   2948
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.22 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.33), residues: 620
  helix:  1.55 (0.38), residues: 166
  sheet:  1.41 (0.55), residues: 64
  loop : -0.70 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.008   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.19 ( 8740)
  covalent geometry    : angle       0.52376 /  0.29 (12510)
  SS BOND              : bond        0.00913 /  0.46 (    2)
  SS BOND              : angle       1.17236 /  0.60 (    4)
  hydrogen bonds       : bond        0.06687 /  4.52 (  313)
  hydrogen bonds       : angle       3.93131 /  2.72 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8490 (mt0) cc_final: 0.7796 (mt0)
REVERT: A  412 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7103 (ttpp)
REVERT: B   72 MET cc_start: 0.8732 (mmm) cc_final: 0.8182 (mmm)
  outliers start: 14
  outliers final: 3
  residues processed: 34
  average time/residue: 0.4261
  time to fit residues: 15.6867
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.092571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.064168 restraints weight = 18020.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.24
r_work: 0.2890 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.0823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8742  Z= 0.171
  Angle     :  0.495   6.060  12514  Z= 0.280
  Chirality :  0.038   0.172   1482
  Planarity :  0.004   0.044   1076
  Dihedral  : 22.004 179.933   2948
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.33), residues: 620
  helix:  1.66 (0.38), residues: 166
  sheet:  1.54 (0.54), residues: 72
  loop : -0.63 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.006   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.17 ( 8740)
  covalent geometry    : angle       0.49445 /  0.28 (12510)
  SS BOND              : bond        0.00868 /  0.44 (    2)
  SS BOND              : angle       1.12715 /  0.58 (    4)
  hydrogen bonds       : bond        0.06293 /  4.25 (  313)
  hydrogen bonds       : angle       3.75813 /  2.60 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8406 (mt0) cc_final: 0.7743 (mt0)
REVERT: A  412 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7118 (ttpp)
REVERT: B   72 MET cc_start: 0.8696 (mmm) cc_final: 0.8079 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 35
  average time/residue: 0.5060
  time to fit residues: 19.0397
Evaluate side-chains
  31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0970
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.092983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.064617 restraints weight = 17765.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.23
r_work: 0.2906 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8742  Z= 0.151
  Angle     :  0.482   7.070  12514  Z= 0.272
  Chirality :  0.037   0.167   1482
  Planarity :  0.004   0.043   1076
  Dihedral  : 21.981 179.948   2948
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 24.19 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.33), residues: 620
  helix:  1.79 (0.38), residues: 166
  sheet:  1.52 (0.56), residues: 64
  loop : -0.63 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.007   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 8740)
  covalent geometry    : angle       0.48137 /  0.27 (12510)
  SS BOND              : bond        0.00809 /  0.41 (    2)
  SS BOND              : angle       1.06934 /  0.55 (    4)
  hydrogen bonds       : bond        0.06043 /  4.08 (  313)
  hydrogen bonds       : angle       3.68671 /  2.55 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  412 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7049 (ttpp)
REVERT: B   72 MET cc_start: 0.8699 (mmm) cc_final: 0.8036 (mmm)
  outliers start: 6
  outliers final: 2
  residues processed: 30
  average time/residue: 0.4863
  time to fit residues: 15.5740
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 47 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 40 optimal weight:    0.4980
   chunk 64 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 68 optimal weight:   20.0000
   overall best weight:    1.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.092507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.064266 restraints weight = 17595.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 2.17
r_work: 0.2900 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.0896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8742  Z= 0.177
  Angle     :  0.497   6.048  12514  Z= 0.279
  Chirality :  0.038   0.171   1482
  Planarity :  0.004   0.043   1076
  Dihedral  : 21.957 179.997   2948
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 24.37 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.33), residues: 620
  helix:  1.80 (0.38), residues: 166
  sheet:  1.51 (0.55), residues: 64
  loop : -0.64 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.008   0.001   TYR A 216 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.008   0.001   TRP B  74 
 HIS   0.004   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.18 ( 8740)
  covalent geometry    : angle       0.49634 /  0.28 (12510)
  SS BOND              : bond        0.00905 /  0.45 (    2)
  SS BOND              : angle       1.16377 /  0.60 (    4)
  hydrogen bonds       : bond        0.06248 /  4.22 (  313)
  hydrogen bonds       : angle       3.70010 /  2.56 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  412 LYS cc_start: 0.7370 (ttpp) cc_final: 0.7166 (ttpp)
REVERT: B   72 MET cc_start: 0.8721 (mmm) cc_final: 0.8040 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 33
  average time/residue: 0.5106
  time to fit residues: 18.0831
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 75 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.091198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.062858 restraints weight = 17884.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 2.17
r_work: 0.2869 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8742  Z= 0.267
  Angle     :  0.568   6.195  12514  Z= 0.313
  Chirality :  0.043   0.181   1482
  Planarity :  0.004   0.045   1076
  Dihedral  : 21.966 179.838   2948
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.37 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.33), residues: 620
  helix:  1.57 (0.38), residues: 166
  sheet:  1.49 (0.54), residues: 72
  loop : -0.71 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 187 
 TYR   0.013   0.001   TYR A 216 
 PHE   0.020   0.002   PHE A  94 
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.002   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.27 ( 8740)
  covalent geometry    : angle       0.56756 /  0.31 (12510)
  SS BOND              : bond        0.01152 /  0.58 (    2)
  SS BOND              : angle       1.46571 /  0.75 (    4)
  hydrogen bonds       : bond        0.07095 /  4.78 (  313)
  hydrogen bonds       : angle       3.83999 /  2.65 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8449 (mtp)
REVERT: A  259 GLN cc_start: 0.8400 (mt0) cc_final: 0.7739 (mt0)
REVERT: A  412 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7252 (ttpp)
REVERT: B   72 MET cc_start: 0.8757 (mmm) cc_final: 0.8077 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 34
  average time/residue: 0.4385
  time to fit residues: 16.0558
Evaluate side-chains
  34 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.093296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064975 restraints weight = 17678.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.21
r_work: 0.2913 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.0983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8742  Z= 0.126
  Angle     :  0.466   5.911  12514  Z= 0.267
  Chirality :  0.036   0.168   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 21.980 179.992   2948
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 25.09 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.33), residues: 620
  helix:  1.85 (0.38), residues: 166
  sheet:  1.63 (0.57), residues: 68
  loop : -0.64 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.005   0.001   TYR A 197 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.13 ( 8740)
  covalent geometry    : angle       0.46576 /  0.27 (12510)
  SS BOND              : bond        0.00735 /  0.37 (    2)
  SS BOND              : angle       1.00812 /  0.52 (    4)
  hydrogen bonds       : bond        0.05915 /  4.00 (  313)
  hydrogen bonds       : angle       3.67749 /  2.55 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8448 (mt0) cc_final: 0.7821 (mt0)
REVERT: A  412 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.7050 (ttpp)
REVERT: B   72 MET cc_start: 0.8703 (mmm) cc_final: 0.8036 (mmm)
  outliers start: 5
  outliers final: 4
  residues processed: 30
  average time/residue: 0.4855
  time to fit residues: 15.5814
Evaluate side-chains
  31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.091898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.063671 restraints weight = 17718.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.16
r_work: 0.2884 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.0892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8742  Z= 0.226
  Angle     :  0.525   6.122  12514  Z= 0.292
  Chirality :  0.040   0.172   1482
  Planarity :  0.004   0.045   1076
  Dihedral  : 21.951 179.833   2948
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 24.55 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.33), residues: 620
  helix:  1.71 (0.38), residues: 166
  sheet:  1.54 (0.54), residues: 72
  loop : -0.64 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.011   0.001   TYR A 216 
 PHE   0.018   0.002   PHE A  94 
 TRP   0.008   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.23 ( 8740)
  covalent geometry    : angle       0.52473 /  0.29 (12510)
  SS BOND              : bond        0.01015 /  0.51 (    2)
  SS BOND              : angle       1.29302 /  0.66 (    4)
  hydrogen bonds       : bond        0.06582 /  4.44 (  313)
  hydrogen bonds       : angle       3.74100 /  2.59 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  412 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7165 (ttpp)
REVERT: B   72 MET cc_start: 0.8732 (mmm) cc_final: 0.8037 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 31
  average time/residue: 0.4797
  time to fit residues: 15.9009
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0770
   chunk 60 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.094324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.066005 restraints weight = 17530.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.22
r_work: 0.2942 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8742  Z= 0.102
  Angle     :  0.442   5.897  12514  Z= 0.254
  Chirality :  0.034   0.163   1482
  Planarity :  0.004   0.043   1076
  Dihedral  : 21.973 179.989   2948
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 24.55 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.33), residues: 620
  helix:  2.11 (0.38), residues: 166
  sheet:  1.73 (0.61), residues: 60
  loop : -0.62 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.008   0.001   TYR B 197 
 PHE   0.017   0.001   PHE B 320 
 TRP   0.009   0.001   TRP B  74 
 HIS   0.002   0.001   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00201 /  0.10 ( 8740)
  covalent geometry    : angle       0.44190 /  0.25 (12510)
  SS BOND              : bond        0.00512 /  0.26 (    2)
  SS BOND              : angle       0.79192 /  0.41 (    4)
  hydrogen bonds       : bond        0.05477 /  3.69 (  313)
  hydrogen bonds       : angle       3.57055 /  2.48 (  742)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8445 (mt0) cc_final: 0.7833 (mt0)
REVERT: A  412 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.7018 (ttpp)
REVERT: B   72 MET cc_start: 0.8652 (mmm) cc_final: 0.7995 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 30
  average time/residue: 0.5248
  time to fit residues: 16.9536
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0040
   chunk 58 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0870
   chunk 62 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   overall best weight:    0.8372

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.094266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.065925 restraints weight = 17742.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.23
r_work: 0.2934 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8742  Z= 0.112
  Angle     :  0.439   6.003  12514  Z= 0.250
  Chirality :  0.035   0.161   1482
  Planarity :  0.004   0.044   1076
  Dihedral  : 21.935 179.879   2948
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 24.55 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.33), residues: 620
  helix:  2.23 (0.38), residues: 166
  sheet:  1.78 (0.62), residues: 60
  loop : -0.56 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 201 
 TYR   0.005   0.001   TYR A 216 
 PHE   0.016   0.001   PHE B 320 
 TRP   0.009   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 8740)
  covalent geometry    : angle       0.43862 /  0.25 (12510)
  SS BOND              : bond        0.00651 /  0.33 (    2)
  SS BOND              : angle       0.78706 /  0.40 (    4)
  hydrogen bonds       : bond        0.05386 /  3.63 (  313)
  hydrogen bonds       : angle       3.52865 /  2.45 (  742)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.64 seconds
wall clock time: 28 minutes 57.44 seconds (1737.44 seconds total)