Starting phenix.real_space_refine
on Sun May  3 04:18:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nyc_49930/05_2026/9nyc_49930.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.066
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      12      5.49       5
     Mg      4      5.21       5
     S      32      5.16       5
     C    6860      2.51       5
     N    1700      2.21       5
     O    1908      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10516
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2569
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 44
          Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1}
          Unresolved non-hydrogen planarities: 37
  Restraints were copied for chains:
    D, B, C
  Time building chain proxies: 2.26, per 1000 atoms: 0.21
  Number of scatterers: 10516
  At special positions: 0
  Unit cell: (110.39, 110.39, 107.07, 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      32     16.00
     P      12     15.00
     Mg      4     11.99
     O    1908      8.00
     N    1700      7.00
     C    6860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 511.2 milliseconds
  

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      57.3% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 30
    Processing helix  chain 'A' and resid 48 through 60
      removed outlier: 3.731A  pdb=" N   GLN A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A  59 " --> pdb=" O   ASP A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 85
    Processing helix  chain 'A' and resid 102 through 113
      removed outlier: 3.992A  pdb=" N   GLU A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 147
    Processing helix  chain 'A' and resid 163 through 171
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 198 through 202
    Processing helix  chain 'A' and resid 208 through 224
      removed outlier: 3.643A  pdb=" N   PHE A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 257
      removed outlier: 5.077A  pdb=" N   TRP A 231 " --> pdb=" O   PRO A 227 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   THR A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 297
      removed outlier: 3.531A  pdb=" N   ALA A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 30
    Processing helix  chain 'D' and resid 48 through 60
      removed outlier: 3.731A  pdb=" N   GLN D  52 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER D  59 " --> pdb=" O   ASP D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 85
    Processing helix  chain 'D' and resid 102 through 113
      removed outlier: 3.992A  pdb=" N   GLU D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 147
    Processing helix  chain 'D' and resid 163 through 171
    Processing helix  chain 'D' and resid 178 through 186
    Processing helix  chain 'D' and resid 198 through 202
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 3.643A  pdb=" N   PHE D 223 " --> pdb=" O   GLY D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 225 through 257
      removed outlier: 5.077A  pdb=" N   TRP D 231 " --> pdb=" O   PRO D 227 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   THR D 232 " --> pdb=" O   LEU D 228 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR D 233 " --> pdb=" O   LYS D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 297
      removed outlier: 3.531A  pdb=" N   ALA D 297 " --> pdb=" O   GLU D 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 30
    Processing helix  chain 'B' and resid 48 through 60
      removed outlier: 3.731A  pdb=" N   GLN B  52 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B  59 " --> pdb=" O   ASP B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 85
    Processing helix  chain 'B' and resid 102 through 113
      removed outlier: 3.992A  pdb=" N   GLU B 106 " --> pdb=" O   GLU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 147
    Processing helix  chain 'B' and resid 163 through 171
    Processing helix  chain 'B' and resid 178 through 186
    Processing helix  chain 'B' and resid 198 through 202
    Processing helix  chain 'B' and resid 208 through 224
      removed outlier: 3.643A  pdb=" N   PHE B 223 " --> pdb=" O   GLY B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 257
      removed outlier: 5.077A  pdb=" N   TRP B 231 " --> pdb=" O   PRO B 227 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   THR B 232 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR B 233 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 297
      removed outlier: 3.531A  pdb=" N   ALA B 297 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 30
    Processing helix  chain 'C' and resid 48 through 60
      removed outlier: 3.731A  pdb=" N   GLN C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER C  59 " --> pdb=" O   ASP C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 85
    Processing helix  chain 'C' and resid 102 through 113
      removed outlier: 3.992A  pdb=" N   GLU C 106 " --> pdb=" O   GLU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 147
    Processing helix  chain 'C' and resid 163 through 171
    Processing helix  chain 'C' and resid 178 through 186
    Processing helix  chain 'C' and resid 198 through 202
    Processing helix  chain 'C' and resid 208 through 224
      removed outlier: 3.643A  pdb=" N   PHE C 223 " --> pdb=" O   GLY C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 257
      removed outlier: 5.077A  pdb=" N   TRP C 231 " --> pdb=" O   PRO C 227 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   THR C 232 " --> pdb=" O   LEU C 228 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR C 233 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 297
      removed outlier: 3.531A  pdb=" N   ALA C 297 " --> pdb=" O   GLU C 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195
      removed outlier: 6.107A  pdb=" N   ILE A 117 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR A 119 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   PHE A 195 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   THR A 121 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   PHE A 158 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ARG A 122 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   GLY A 156 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG A 159 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   SER A   6 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 307
      removed outlier: 6.510A  pdb=" N   SER B   6 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG B 159 " --> pdb=" O   PRO B  92 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   GLY B 156 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ARG B 122 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   PHE B 158 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ILE B 117 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL B 193 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR B 119 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   PHE B 195 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   THR B 121 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 190 through 195
      removed outlier: 6.107A  pdb=" N   ILE D 117 " --> pdb=" O   THR D 191 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL D 193 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR D 119 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   PHE D 195 " --> pdb=" O   TYR D 119 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   THR D 121 " --> pdb=" O   PHE D 195 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   PHE D 158 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ARG D 122 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   GLY D 156 " --> pdb=" O   ARG D 122 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG D 159 " --> pdb=" O   PRO D  92 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   SER D   6 " --> pdb=" O   ILE D  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 303 through 307
      removed outlier: 6.510A  pdb=" N   SER C   6 " --> pdb=" O   ILE C  91 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG C 159 " --> pdb=" O   PRO C  92 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   GLY C 156 " --> pdb=" O   ARG C 122 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ARG C 122 " --> pdb=" O   GLY C 156 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   PHE C 158 " --> pdb=" O   ALA C 120 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ILE C 117 " --> pdb=" O   THR C 191 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL C 193 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR C 119 " --> pdb=" O   VAL C 193 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   PHE C 195 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   THR C 121 " --> pdb=" O   PHE C 195 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1776 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1648
        1.29 -     1.42: 2784
        1.42 -     1.55: 6244
        1.55 -     1.68: 24
        1.68 -     1.80: 60
  Bond restraints: 10760
  Sorted by residual:
  bond pdb=" C4C UPG B 401 "
       pdb=" O4C UPG B 401 "
    ideal  model  delta    sigma   weight residual
    1.431  1.669 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C4C UPG C 401 "
       pdb=" O4C UPG C 401 "
    ideal  model  delta    sigma   weight residual
    1.431  1.669 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C4C UPG D 401 "
       pdb=" O4C UPG D 401 "
    ideal  model  delta    sigma   weight residual
    1.431  1.669 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" C4C UPG A 401 "
       pdb=" O4C UPG A 401 "
    ideal  model  delta    sigma   weight residual
    1.431  1.669 -0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" O02 5TR D 402 "
       pdb=" P01 5TR D 402 "
    ideal  model  delta    sigma   weight residual
    1.824  1.621  0.203 2.00e-02 2.50e+03 1.03e+02
  ... (remaining 10755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 14492
        3.24 -     6.48: 84
        6.48 -     9.72: 20
        9.72 -    12.96: 12
       12.96 -    16.20: 4
  Bond angle restraints: 14612
  Sorted by residual:
  angle pdb=" O04 5TR C 402 "
        pdb=" P01 5TR C 402 "
        pdb=" O05 5TR C 402 "
      ideal   model   delta    sigma   weight residual
     129.39  113.19   16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" O04 5TR B 402 "
        pdb=" P01 5TR B 402 "
        pdb=" O05 5TR B 402 "
      ideal   model   delta    sigma   weight residual
     129.39  113.19   16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" O04 5TR D 402 "
        pdb=" P01 5TR D 402 "
        pdb=" O05 5TR D 402 "
      ideal   model   delta    sigma   weight residual
     129.39  113.19   16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" O04 5TR A 402 "
        pdb=" P01 5TR A 402 "
        pdb=" O05 5TR A 402 "
      ideal   model   delta    sigma   weight residual
     129.39  113.19   16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" O1A UPG B 401 "
        pdb=" PA  UPG B 401 "
        pdb=" O2A UPG B 401 "
      ideal   model   delta    sigma   weight residual
     121.98  109.21   12.77 3.00e+00 1.11e-01 1.81e+01
  ... (remaining 14607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.66: 5760
       24.66 -    49.31: 552
       49.31 -    73.97: 172
       73.97 -    98.62: 20
       98.62 -   123.28: 24
  Dihedral angle restraints: 6528
    sinusoidal: 2844
      harmonic: 3684
  Sorted by residual:
  dihedral pdb=" C5' UPG B 401 "
           pdb=" C1' UPG B 401 "
           pdb=" O5' UPG B 401 "
           pdb=" O3B UPG B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.15  174.87  123.28     1      3.00e+01 1.11e-03 1.65e+01
  dihedral pdb=" C5' UPG A 401 "
           pdb=" C1' UPG A 401 "
           pdb=" O5' UPG A 401 "
           pdb=" O3B UPG A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.15  174.87  123.28     1      3.00e+01 1.11e-03 1.65e+01
  dihedral pdb=" C5' UPG C 401 "
           pdb=" C1' UPG C 401 "
           pdb=" O5' UPG C 401 "
           pdb=" O3B UPG C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.15  174.87  123.28     1      3.00e+01 1.11e-03 1.65e+01
  ... (remaining 6525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1288
       0.049 -    0.098: 272
       0.098 -    0.147: 72
       0.147 -    0.196: 0
       0.196 -    0.245: 4
  Chirality restraints: 1636
  Sorted by residual:
  chirality pdb=" C3C UPG C 401 "
            pdb=" C2C UPG C 401 "
            pdb=" C4C UPG C 401 "
            pdb=" O3C UPG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" C3C UPG B 401 "
            pdb=" C2C UPG B 401 "
            pdb=" C4C UPG B 401 "
            pdb=" O3C UPG B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" C3C UPG D 401 "
            pdb=" C2C UPG D 401 "
            pdb=" C4C UPG D 401 "
            pdb=" O3C UPG D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1633 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  91 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO C  92 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C  92 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  92 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  91 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO D  92 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D  92 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  92 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  91 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO B  92 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B  92 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  92 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 88
        2.54 -     3.13: 7884
        3.13 -     3.72: 17104
        3.72 -     4.31: 24572
        4.31 -     4.90: 40318
  Nonbonded interactions: 89966
  Sorted by model distance:
  nonbonded pdb=" O2B UPG A 401 "
            pdb="MG    MG A 403 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" O2B UPG D 401 "
            pdb="MG    MG D 403 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" O2B UPG B 401 "
            pdb="MG    MG B 403 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" O2B UPG C 401 "
            pdb="MG    MG C 403 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" OD2 ASP A  96 "
            pdb="MG    MG A 403 "
     model   vdw
     2.075 2.170
  ... (remaining 89961 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.540
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.600
  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:9.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
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      :  0.011   0.238  10760  Z= 0.565
  Angle     :  0.775  16.199  14612  Z= 0.321
  Chirality :  0.043   0.245   1636
  Planarity :  0.004   0.037   1796
  Dihedral  : 21.813 123.277   4168
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 21.40 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.95 (0.24), residues: 1256
  helix:  1.52 (0.20), residues: 688
  sheet: -0.17 (0.40), residues: 164
  loop : -0.47 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.007   0.001   TYR B  84 
 PHE   0.010   0.001   PHE A 223 
 TRP   0.008   0.001   TRP A 231 
 HIS   0.004   0.002   HIS D 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.01137 (10760)
  covalent geometry    : angle       0.77511 (14612)
  hydrogen bonds       : bond        0.08191 (  600)
  hydrogen bonds       : angle       5.97036 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.329 
Fit side-chains
  outliers start: 10
  outliers final: 10
  residues processed: 134
  average time/residue: 0.7134
  time to fit residues: 101.6712
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue  252 LYS
Chi-restraints excluded: chain D residue   59 SER
Chi-restraints excluded: chain D residue  252 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  252 LYS
Chi-restraints excluded: chain C residue   59 SER
Chi-restraints excluded: chain C residue  252 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.0370
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.9860

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
B  52 GLN
C  52 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.113402 restraints weight = 10923.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.64
r_work: 0.3129 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.0542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10760  Z= 0.125
  Angle     :  0.485   6.696  14612  Z= 0.245
  Chirality :  0.043   0.235   1636
  Planarity :  0.004   0.033   1796
  Dihedral  : 16.910  90.132   1704
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.81 %
    Favored  : 78.78 %
  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:  1.37 (0.25), residues: 1256
  helix:  1.92 (0.20), residues: 704
  sheet: -0.28 (0.40), residues: 164
  loop : -0.38 (0.34), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 TYR   0.007   0.001   TYR B  57 
 PHE   0.009   0.001   PHE D 223 
 TRP   0.005   0.001   TRP B 231 
 HIS   0.004   0.001   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10760)
  covalent geometry    : angle       0.48462 (14612)
  hydrogen bonds       : bond        0.03565 (  600)
  hydrogen bonds       : angle       4.40125 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  126 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.5182 (tm-30)
REVERT: A  129 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6828 (t)
REVERT: D  126 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.5195 (tm-30)
REVERT: D  129 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6850 (t)
REVERT: B  126 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.5180 (tm-30)
REVERT: B  129 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6844 (t)
REVERT: C  126 GLN cc_start: 0.5950 (OUTLIER) cc_final: 0.5198 (tm-30)
REVERT: C  129 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6862 (t)
  outliers start: 38
  outliers final: 4
  residues processed: 150
  average time/residue: 0.7183
  time to fit residues: 114.5591
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  255 THR
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  129 THR
Chi-restraints excluded: chain C residue  255 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
B  52 GLN
B  86 GLN
C  52 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.148396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108466 restraints weight = 10953.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.65
r_work: 0.3058 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  10760  Z= 0.278
  Angle     :  0.584   7.432  14612  Z= 0.296
  Chirality :  0.048   0.246   1636
  Planarity :  0.006   0.062   1796
  Dihedral  : 15.932  79.971   1676
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.90 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), residues: 1256
  helix:  1.77 (0.20), residues: 696
  sheet: -0.25 (0.40), residues: 164
  loop : -0.51 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  70 
 TYR   0.011   0.002   TYR D  84 
 PHE   0.015   0.002   PHE C 223 
 TRP   0.008   0.001   TRP A 111 
 HIS   0.004   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 (10760)
  covalent geometry    : angle       0.58428 (14612)
  hydrogen bonds       : bond        0.04320 (  600)
  hydrogen bonds       : angle       4.46904 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A   11 MET cc_start: 0.9251 (mtt) cc_final: 0.9016 (mtt)
REVERT: A  211 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7162 (mptt)
REVERT: D   11 MET cc_start: 0.9255 (mtt) cc_final: 0.9018 (mtt)
REVERT: D  211 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7146 (mptt)
REVERT: B   11 MET cc_start: 0.9251 (mtt) cc_final: 0.9014 (mtt)
REVERT: B  211 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7176 (mptt)
REVERT: C   11 MET cc_start: 0.9250 (mtt) cc_final: 0.9012 (mtt)
REVERT: C  211 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7154 (mptt)
  outliers start: 33
  outliers final: 12
  residues processed: 132
  average time/residue: 0.6457
  time to fit residues: 91.1715
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain D residue  255 THR
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue  211 LYS
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  258 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 121 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 123 optimal weight:    0.0060
   chunk 111 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
C  52 GLN
C  86 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.152954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113590 restraints weight = 11017.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.64
r_work: 0.3126 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.0801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  10760  Z= 0.108
  Angle     :  0.485   7.433  14612  Z= 0.242
  Chirality :  0.044   0.319   1636
  Planarity :  0.003   0.028   1796
  Dihedral  : 12.611  57.418   1676
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.99 %
    Favored  : 79.86 %
  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:  1.58 (0.25), residues: 1256
  helix:  2.28 (0.20), residues: 676
  sheet: -0.35 (0.41), residues: 164
  loop : -0.39 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.006   0.001   TYR B 209 
 PHE   0.011   0.001   PHE C 223 
 TRP   0.007   0.001   TRP B 111 
 HIS   0.002   0.001   HIS D 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10760)
  covalent geometry    : angle       0.48457 (14612)
  hydrogen bonds       : bond        0.03340 (  600)
  hydrogen bonds       : angle       4.11538 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8614 (mp0) cc_final: 0.8400 (mp0)
REVERT: A  129 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6886 (t)
REVERT: A  138 MET cc_start: 0.8669 (mmp) cc_final: 0.8355 (mmm)
REVERT: D  102 GLU cc_start: 0.8605 (mp0) cc_final: 0.8389 (mp0)
REVERT: D  129 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6888 (t)
REVERT: D  138 MET cc_start: 0.8676 (mmp) cc_final: 0.8363 (mmm)
REVERT: B  102 GLU cc_start: 0.8605 (mp0) cc_final: 0.8387 (mp0)
REVERT: B  129 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6909 (t)
REVERT: B  138 MET cc_start: 0.8669 (mmp) cc_final: 0.8356 (mmm)
REVERT: C  102 GLU cc_start: 0.8604 (mp0) cc_final: 0.8387 (mp0)
REVERT: C  129 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6906 (t)
REVERT: C  138 MET cc_start: 0.8677 (mmp) cc_final: 0.8368 (mmm)
  outliers start: 24
  outliers final: 2
  residues processed: 136
  average time/residue: 0.7239
  time to fit residues: 104.5248
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue  129 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 105 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.152253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.112684 restraints weight = 10996.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.64
r_work: 0.3113 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.0864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10760  Z= 0.134
  Angle     :  0.463   4.875  14612  Z= 0.240
  Chirality :  0.043   0.254   1636
  Planarity :  0.004   0.033   1796
  Dihedral  : 10.681  58.324   1676
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.35 %
    Favored  : 79.86 %
  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:  1.62 (0.25), residues: 1256
  helix:  2.34 (0.20), residues: 676
  sheet: -0.36 (0.41), residues: 164
  loop : -0.42 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 163 
 TYR   0.008   0.001   TYR B  57 
 PHE   0.011   0.001   PHE B 223 
 TRP   0.006   0.001   TRP B 111 
 HIS   0.004   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10760)
  covalent geometry    : angle       0.46320 (14612)
  hydrogen bonds       : bond        0.03435 (  600)
  hydrogen bonds       : angle       4.06274 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8611 (mp0) cc_final: 0.8382 (mp0)
REVERT: A  126 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5219 (tm-30)
REVERT: A  211 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7238 (mptt)
REVERT: D  102 GLU cc_start: 0.8598 (mp0) cc_final: 0.8372 (mp0)
REVERT: D  126 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5220 (tm-30)
REVERT: D  211 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7238 (mptt)
REVERT: B  102 GLU cc_start: 0.8604 (mp0) cc_final: 0.8376 (mp0)
REVERT: B  126 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5227 (tm-30)
REVERT: B  211 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7242 (mptt)
REVERT: C  102 GLU cc_start: 0.8595 (mp0) cc_final: 0.8365 (mp0)
REVERT: C  126 GLN cc_start: 0.5976 (OUTLIER) cc_final: 0.5223 (tm-30)
REVERT: C  211 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7232 (mptt)
  outliers start: 20
  outliers final: 0
  residues processed: 133
  average time/residue: 0.7194
  time to fit residues: 101.7508
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  211 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0370
   chunk 53 optimal weight:    6.9990
   chunk 92 optimal weight:    0.8980
   chunk 119 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 277 GLN
D  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.115674 restraints weight = 11017.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.64
r_work: 0.3156 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10760  Z= 0.099
  Angle     :  0.420   4.451  14612  Z= 0.223
  Chirality :  0.040   0.138   1636
  Planarity :  0.003   0.026   1796
  Dihedral  :  9.885  59.904   1676
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.17 %
    Favored  : 80.58 %
  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:  1.77 (0.25), residues: 1256
  helix:  2.43 (0.20), residues: 684
  sheet: -0.33 (0.42), residues: 164
  loop : -0.32 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 123 
 TYR   0.006   0.001   TYR B  57 
 PHE   0.010   0.001   PHE B 223 
 TRP   0.006   0.001   TRP A 111 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (10760)
  covalent geometry    : angle       0.41969 (14612)
  hydrogen bonds       : bond        0.03072 (  600)
  hydrogen bonds       : angle       3.92346 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8586 (mp0) cc_final: 0.8373 (mp0)
REVERT: A  126 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5193 (tm-30)
REVERT: A  211 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7203 (mptt)
REVERT: D  102 GLU cc_start: 0.8580 (mp0) cc_final: 0.8371 (mp0)
REVERT: D  126 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5203 (tm-30)
REVERT: D  211 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7203 (mptt)
REVERT: B  102 GLU cc_start: 0.8586 (mp0) cc_final: 0.8367 (mp0)
REVERT: B  126 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5196 (tm-30)
REVERT: B  211 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7215 (mptt)
REVERT: C  102 GLU cc_start: 0.8572 (mp0) cc_final: 0.8358 (mp0)
REVERT: C  126 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5204 (tm-30)
REVERT: C  211 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7193 (mptt)
  outliers start: 14
  outliers final: 0
  residues processed: 138
  average time/residue: 0.7515
  time to fit residues: 109.9983
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  211 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    0.0020
   chunk 111 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0870
   chunk 22 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.4172

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
D 277 GLN
C  52 GLN
C 277 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.150569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110813 restraints weight = 10914.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.64
r_work: 0.3084 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  10760  Z= 0.206
  Angle     :  0.489   4.494  14612  Z= 0.258
  Chirality :  0.043   0.136   1636
  Planarity :  0.004   0.043   1796
  Dihedral  : 10.030  58.847   1676
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.08 %
    Favored  : 79.32 %
  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:  1.52 (0.25), residues: 1256
  helix:  2.25 (0.20), residues: 676
  sheet: -0.32 (0.41), residues: 164
  loop : -0.48 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 163 
 TYR   0.010   0.002   TYR A  84 
 PHE   0.013   0.001   PHE B 223 
 TRP   0.007   0.001   TRP D 111 
 HIS   0.003   0.001   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10760)
  covalent geometry    : angle       0.48892 (14612)
  hydrogen bonds       : bond        0.03775 (  600)
  hydrogen bonds       : angle       4.15000 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  126 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5201 (tm-30)
REVERT: A  211 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7268 (mptt)
REVERT: D  126 GLN cc_start: 0.5971 (OUTLIER) cc_final: 0.5205 (tm-30)
REVERT: D  211 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7264 (mptt)
REVERT: B  126 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5203 (tm-30)
REVERT: B  211 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7288 (mptt)
REVERT: C  126 GLN cc_start: 0.5971 (OUTLIER) cc_final: 0.5203 (tm-30)
REVERT: C  211 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7267 (mptt)
  outliers start: 29
  outliers final: 4
  residues processed: 133
  average time/residue: 0.6942
  time to fit residues: 98.3421
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain D residue  258 VAL
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  211 LYS
Chi-restraints excluded: chain C residue  258 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 119 optimal weight:   10.0000
   chunk 97 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0970
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
C  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.153031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113598 restraints weight = 10915.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.64
r_work: 0.3124 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10760  Z= 0.117
  Angle     :  0.431   4.425  14612  Z= 0.231
  Chirality :  0.041   0.138   1636
  Planarity :  0.003   0.026   1796
  Dihedral  :  9.717  59.866   1676
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.26 %
    Favored  : 79.77 %
  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:  1.67 (0.25), residues: 1256
  helix:  2.38 (0.20), residues: 676
  sheet: -0.29 (0.42), residues: 164
  loop : -0.43 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 123 
 TYR   0.007   0.001   TYR B  57 
 PHE   0.011   0.001   PHE A 223 
 TRP   0.007   0.001   TRP A 111 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10760)
  covalent geometry    : angle       0.43137 (14612)
  hydrogen bonds       : bond        0.03269 (  600)
  hydrogen bonds       : angle       4.02589 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  126 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5192 (tm-30)
REVERT: A  211 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7243 (mptt)
REVERT: D  126 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5191 (tm-30)
REVERT: D  211 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7244 (mptt)
REVERT: B  126 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5196 (tm-30)
REVERT: B  211 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7256 (mptt)
REVERT: C  126 GLN cc_start: 0.5968 (OUTLIER) cc_final: 0.5200 (tm-30)
REVERT: C  211 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7242 (mptt)
  outliers start: 22
  outliers final: 0
  residues processed: 140
  average time/residue: 0.6477
  time to fit residues: 97.0582
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain B residue  126 GLN
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  211 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   chunk 104 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 108 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
C  52 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.154622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.115341 restraints weight = 10896.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.66
r_work: 0.3137 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10760  Z= 0.102
  Angle     :  0.412   4.454  14612  Z= 0.222
  Chirality :  0.040   0.135   1636
  Planarity :  0.003   0.023   1796
  Dihedral  :  9.487  58.983   1676
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 19.42 %
    Favored  : 79.32 %
  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:  1.79 (0.25), residues: 1256
  helix:  2.43 (0.20), residues: 684
  sheet: -0.27 (0.42), residues: 164
  loop : -0.31 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 123 
 TYR   0.006   0.001   TYR B  57 
 PHE   0.010   0.001   PHE B 223 
 TRP   0.006   0.001   TRP A 111 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (10760)
  covalent geometry    : angle       0.41235 (14612)
  hydrogen bonds       : bond        0.03098 (  600)
  hydrogen bonds       : angle       3.90358 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7176 (mptt)
REVERT: D  211 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7192 (mptt)
REVERT: B  211 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7197 (mptt)
REVERT: C  211 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7184 (mptt)
  outliers start: 14
  outliers final: 0
  residues processed: 129
  average time/residue: 0.7466
  time to fit residues: 102.1747
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain C residue  211 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN
B 277 GLN
C  52 GLN
C  86 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.152785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.113079 restraints weight = 10910.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.67
r_work: 0.3115 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10760  Z= 0.135
  Angle     :  0.436   4.470  14612  Z= 0.235
  Chirality :  0.041   0.137   1636
  Planarity :  0.004   0.027   1796
  Dihedral  :  9.402  58.496   1676
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 19.87 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.69 (0.25), residues: 1256
  helix:  2.33 (0.20), residues: 684
  sheet: -0.27 (0.42), residues: 164
  loop : -0.34 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 123 
 TYR   0.008   0.001   TYR B  84 
 PHE   0.010   0.001   PHE B 223 
 TRP   0.006   0.001   TRP B 111 
 HIS   0.004   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10760)
  covalent geometry    : angle       0.43628 (14612)
  hydrogen bonds       : bond        0.03347 (  600)
  hydrogen bonds       : angle       3.99132 ( 1776)

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

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

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2512 Ramachandran restraints generated.
    1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7223 (mptt)
REVERT: D  211 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7226 (mptt)
REVERT: B  211 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7229 (mptt)
REVERT: C  211 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7225 (mptt)
  outliers start: 8
  outliers final: 4
  residues processed: 120
  average time/residue: 0.6672
  time to fit residues: 85.5045
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue  211 LYS
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  211 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 119 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
D  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.150348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.110475 restraints weight = 10943.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.63
r_work: 0.3069 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  10760  Z= 0.218
  Angle     :  0.496   4.533  14612  Z= 0.264
  Chirality :  0.043   0.136   1636
  Planarity :  0.005   0.047   1796
  Dihedral  :  9.517  56.664   1676
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 19.24 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.52 (0.25), residues: 1256
  helix:  2.21 (0.20), residues: 676
  sheet: -0.25 (0.42), residues: 164
  loop : -0.44 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 163 
 TYR   0.011   0.002   TYR B  57 
 PHE   0.013   0.002   PHE D 223 
 TRP   0.007   0.001   TRP A 111 
 HIS   0.004   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (10760)
  covalent geometry    : angle       0.49631 (14612)
  hydrogen bonds       : bond        0.03842 (  600)
  hydrogen bonds       : angle       4.15748 ( 1776)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3987.20 seconds
wall clock time: 68 minutes 38.46 seconds (4118.46 seconds total)