Starting phenix.real_space_refine
on Thu Feb  5 02:07:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kbk_62228/02_2026/9kbk_62228.cif"
  }
  resolution = 3.48
  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=   0.087 sd=   0.879
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8028 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    5121      2.51       5
     N    1343      2.21       5
     O    1592      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8086
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2490
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 318}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1556
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 2490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2490
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 318}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 1550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1550
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 1.97, per 1000 atoms: 0.24
  Number of scatterers: 8086
  At special positions: 0
  Unit cell: (125.25, 93.75, 97.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1592      8.00
     N    1343      7.00
     C    5121      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: 0.75
  Conformation dependent library (CDL) restraints added in 342.2 milliseconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      67.3% alpha, 12.1% 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 91 through 97
    Processing helix  chain 'A' and resid 99 through 114
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 135 through 152
    Processing helix  chain 'A' and resid 158 through 182
      removed outlier: 3.758A  pdb=" N   GLN A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 185
      No H-bonds generated for 'chain 'A' and resid 183 through 185'
    Processing helix  chain 'A' and resid 193 through 199
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 4.089A  pdb=" N   GLU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 246
      removed outlier: 3.932A  pdb=" N   ALA A 245 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 266
    Processing helix  chain 'A' and resid 266 through 282
      removed outlier: 3.757A  pdb=" N   ILE A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 313
      removed outlier: 3.666A  pdb=" N   PHE A 311 " --> pdb=" O   ASP A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
    Processing helix  chain 'A' and resid 323 through 329
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.724A  pdb=" N   GLN A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 351
      removed outlier: 3.758A  pdb=" N   ARG A 346 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 370
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 3.569A  pdb=" N   ARG A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'B' and resid 83 through 97
      removed outlier: 3.513A  pdb=" N   GLU B  97 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 103
      removed outlier: 3.506A  pdb=" N   ILE B 103 " --> pdb=" O   ASN B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 124
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 3.509A  pdb=" N   LEU B 134 " --> pdb=" O   THR B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 159
    Processing helix  chain 'B' and resid 224 through 232
    Processing helix  chain 'B' and resid 234 through 242
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'C' and resid 99 through 114
    Processing helix  chain 'C' and resid 118 through 130
    Processing helix  chain 'C' and resid 135 through 152
    Processing helix  chain 'C' and resid 158 through 182
      removed outlier: 3.757A  pdb=" N   GLN C 162 " --> pdb=" O   THR C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 185
      No H-bonds generated for 'chain 'C' and resid 183 through 185'
    Processing helix  chain 'C' and resid 193 through 199
    Processing helix  chain 'C' and resid 199 through 222
      removed outlier: 4.089A  pdb=" N   GLU C 222 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 246
      removed outlier: 3.932A  pdb=" N   ALA C 245 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER C 246 " --> pdb=" O   ILE C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 266
    Processing helix  chain 'C' and resid 266 through 282
      removed outlier: 3.758A  pdb=" N   ILE C 270 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 313
      removed outlier: 3.666A  pdb=" N   PHE C 311 " --> pdb=" O   ASP C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 318
    Processing helix  chain 'C' and resid 323 through 329
    Processing helix  chain 'C' and resid 332 through 340
      removed outlier: 3.724A  pdb=" N   GLN C 340 " --> pdb=" O   ILE C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 351
      removed outlier: 3.758A  pdb=" N   ARG C 346 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 370
    Processing helix  chain 'C' and resid 370 through 390
      removed outlier: 3.569A  pdb=" N   ARG C 374 " --> pdb=" O   GLY C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 397 through 412
    Processing helix  chain 'D' and resid 83 through 97
    Processing helix  chain 'D' and resid 99 through 103
    Processing helix  chain 'D' and resid 107 through 124
    Processing helix  chain 'D' and resid 129 through 134
      removed outlier: 3.592A  pdb=" N   LEU D 134 " --> pdb=" O   THR D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 159
      removed outlier: 3.728A  pdb=" N   ARG D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 232
    Processing helix  chain 'D' and resid 234 through 242
    Processing sheet with id=AA1, first strand: chain 'B' and resid 174 through 175
      removed outlier: 6.805A  pdb=" N   GLN B 198 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ILE B 222 " --> pdb=" O   GLN B 198 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   THR B 200 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   SER B 220 " --> pdb=" O   THR B 200 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   GLU B 202 " --> pdb=" O   ASP B 218 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLU B 271 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   LEU B 144 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
      removed outlier: 5.351A  pdb=" N   PHE B 170 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 10.810A  pdb=" N   TYR B 146 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 14.500A  pdb=" N   GLY B 168 " --> pdb=" O   TYR B 146 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LYS B 186 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   PHE B 170 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL B 184 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 174 through 175
      removed outlier: 6.755A  pdb=" N   GLN D 198 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ILE D 222 " --> pdb=" O   GLN D 198 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   THR D 200 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   SER D 220 " --> pdb=" O   THR D 200 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   GLU D 202 " --> pdb=" O   ASP D 218 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLU D 271 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   LEU D 144 " --> pdb=" O   GLU D 271 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   PHE D 170 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 11.132A  pdb=" N   TYR D 146 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 14.718A  pdb=" N   GLY D 168 " --> pdb=" O   TYR D 146 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LYS D 186 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE D 170 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   VAL D 184 " --> pdb=" O   PHE D 170 " (cutoff:3.500A)

    538 hydrogen bonds defined for protein.
    1563 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: 1.33

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2695
        1.34 -     1.46: 1332
        1.46 -     1.57: 4119
        1.57 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 8198
  Sorted by residual:
  bond pdb=" N   GLY C 186 "
       pdb=" CA  GLY C 186 "
    ideal  model  delta    sigma   weight residual
    1.445  1.480 -0.035 9.90e-03 1.02e+04 1.28e+01
  bond pdb=" CA  SER B 123 "
       pdb=" CB  SER B 123 "
    ideal  model  delta    sigma   weight residual
    1.531  1.485  0.046 1.59e-02 3.96e+03 8.33e+00
  bond pdb=" CA  THR A 193 "
       pdb=" C   THR A 193 "
    ideal  model  delta    sigma   weight residual
    1.528  1.490  0.037 1.37e-02 5.33e+03 7.47e+00
  bond pdb=" CA  THR C 193 "
       pdb=" C   THR C 193 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.030 1.23e-02 6.61e+03 5.83e+00
  bond pdb=" N   MET A 187 "
       pdb=" CA  MET A 187 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.64e+00
  ... (remaining 8193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 10709
        1.90 -     3.80: 316
        3.80 -     5.71: 44
        5.71 -     7.61: 8
        7.61 -     9.51: 4
  Bond angle restraints: 11081
  Sorted by residual:
  angle pdb=" N   THR A 193 "
        pdb=" CA  THR A 193 "
        pdb=" CB  THR A 193 "
      ideal   model   delta    sigma   weight residual
     110.44  100.93    9.51 1.43e+00 4.89e-01 4.42e+01
  angle pdb=" N   ARG A 189 "
        pdb=" CA  ARG A 189 "
        pdb=" C   ARG A 189 "
      ideal   model   delta    sigma   weight residual
     111.54  102.59    8.95 1.36e+00 5.41e-01 4.33e+01
  angle pdb=" C   SER C 185 "
        pdb=" N   GLY C 186 "
        pdb=" CA  GLY C 186 "
      ideal   model   delta    sigma   weight residual
     121.82  116.49    5.33 8.40e-01 1.42e+00 4.03e+01
  angle pdb=" N   GLY C 186 "
        pdb=" CA  GLY C 186 "
        pdb=" C   GLY C 186 "
      ideal   model   delta    sigma   weight residual
     111.14  119.90   -8.76 1.46e+00 4.69e-01 3.60e+01
  angle pdb=" N   THR C 193 "
        pdb=" CA  THR C 193 "
        pdb=" CB  THR C 193 "
      ideal   model   delta    sigma   weight residual
     109.92  101.61    8.31 1.60e+00 3.91e-01 2.70e+01
  ... (remaining 11076 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4475
       17.66 -    35.33: 429
       35.33 -    52.99: 79
       52.99 -    70.65: 24
       70.65 -    88.32: 6
  Dihedral angle restraints: 5013
    sinusoidal: 1981
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" CA  LEU B 217 "
           pdb=" C   LEU B 217 "
           pdb=" N   ASP B 218 "
           pdb=" CA  ASP B 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.84   28.16     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" N   THR A 193 "
           pdb=" C   THR A 193 "
           pdb=" CA  THR A 193 "
           pdb=" CB  THR A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  110.49   12.91     0      2.50e+00 1.60e-01 2.67e+01
  dihedral pdb=" N   THR C 193 "
           pdb=" C   THR C 193 "
           pdb=" CA  THR C 193 "
           pdb=" CB  THR C 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  111.49   11.91     0      2.50e+00 1.60e-01 2.27e+01
  ... (remaining 5010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1003
       0.051 -    0.101: 253
       0.101 -    0.152: 43
       0.152 -    0.202: 10
       0.202 -    0.253: 3
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" CB  ILE D 201 "
            pdb=" CA  ILE D 201 "
            pdb=" CG1 ILE D 201 "
            pdb=" CG2 ILE D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  GLU B 119 "
            pdb=" N   GLU B 119 "
            pdb=" C   GLU B 119 "
            pdb=" CB  GLU B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  LEU B 120 "
            pdb=" N   LEU B 120 "
            pdb=" C   LEU B 120 "
            pdb=" CB  LEU B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1309 not shown)

  Planarity restraints: 1423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 217 "   -0.015 2.00e-02 2.50e+03   3.06e-02 9.38e+00
        pdb=" C   LEU B 217 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LEU B 217 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASP B 218 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 186 "   -0.013 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   GLY A 186 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLY A 186 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 187 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 252 "    0.012 2.00e-02 2.50e+03   2.51e-02 6.29e+00
        pdb=" CG  ASP A 252 "   -0.043 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 252 "    0.016 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 252 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1420 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1414
        2.75 -     3.28: 9201
        3.28 -     3.82: 13726
        3.82 -     4.36: 15684
        4.36 -     4.90: 25845
  Nonbonded interactions: 65870
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 274 "
            pdb=" OG  SER D 276 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASP B 274 "
            pdb=" OG  SER B 276 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER D 220 "
            pdb=" OH  TYR D 235 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ASP B 132 "
            pdb=" NE2 GLN B 135 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OG1 THR B 209 "
            pdb=" O   LYS B 212 "
     model   vdw
     2.261 3.040
  ... (remaining 65865 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'B' and (resid 82 through 260 or (resid 261 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 262 through 278))
  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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.840
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
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      :  0.007   0.046   8198  Z= 0.336
  Angle     :  0.793   9.509  11081  Z= 0.478
  Chirality :  0.047   0.253   1312
  Planarity :  0.004   0.052   1423
  Dihedral  : 14.768  88.317   3045
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.43 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.83 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -1.21 (0.25), residues: 1036
  helix:  0.61 (0.19), residues: 644
  sheet: -2.49 (0.43), residues: 124
  loop : -3.38 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 258 
 TYR   0.011   0.001   TYR B 205 
 PHE   0.011   0.002   PHE A 302 
 TRP   0.008   0.002   TRP D 142 
 HIS   0.012   0.002   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00709 ( 8198)
  covalent geometry    : angle       0.79268 (11081)
  hydrogen bonds       : bond        0.14572 (  538)
  hydrogen bonds       : angle       5.95008 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8222 (m)
REVERT: B  106 MET cc_start: 0.7716 (tpp) cc_final: 0.7486 (tpp)
REVERT: B  142 TRP cc_start: 0.8413 (m100) cc_final: 0.7886 (m100)
REVERT: B  146 TYR cc_start: 0.9177 (t80) cc_final: 0.8945 (t80)
REVERT: B  172 GLN cc_start: 0.9094 (tt0) cc_final: 0.8869 (tp40)
REVERT: B  243 ASN cc_start: 0.8717 (p0) cc_final: 0.8403 (p0)
REVERT: B  247 TRP cc_start: 0.9305 (p-90) cc_final: 0.9013 (p-90)
REVERT: B  252 TYR cc_start: 0.7949 (t80) cc_final: 0.7713 (t80)
REVERT: B  266 ASN cc_start: 0.8907 (m110) cc_final: 0.8567 (m110)
REVERT: C  396 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8740 (t)
REVERT: D  142 TRP cc_start: 0.8217 (m100) cc_final: 0.7324 (m100)
REVERT: D  171 PHE cc_start: 0.9099 (m-80) cc_final: 0.8846 (m-10)
REVERT: D  172 GLN cc_start: 0.9218 (tt0) cc_final: 0.8701 (tp-100)
REVERT: D  243 ASN cc_start: 0.8657 (p0) cc_final: 0.8308 (p0)
REVERT: D  252 TYR cc_start: 0.7806 (t80) cc_final: 0.7533 (t80)
REVERT: D  266 ASN cc_start: 0.9067 (m110) cc_final: 0.8731 (m-40)
  outliers start: 19
  outliers final: 8
  residues processed: 178
  average time/residue: 0.1475
  time to fit residues: 32.2584
Evaluate side-chains
  128 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  191 LYS
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  396 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 213 GLN
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN
C 213 GLN
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.059220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.044268 restraints weight = 35799.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2496 rms_B_bonded: 3.81
r_work: 0.2311 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8198  Z= 0.145
  Angle     :  0.637   7.620  11081  Z= 0.335
  Chirality :  0.041   0.155   1312
  Planarity :  0.005   0.058   1423
  Dihedral  :  6.119  51.744   1126
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.38 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.59 (0.27), residues: 1036
  helix:  2.00 (0.20), residues: 658
  sheet: -1.72 (0.45), residues: 134
  loop : -2.98 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 395 
 TYR   0.014   0.001   TYR D 146 
 PHE   0.020   0.001   PHE B 171 
 TRP   0.013   0.002   TRP D 247 
 HIS   0.009   0.002   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8198)
  covalent geometry    : angle       0.63665 (11081)
  hydrogen bonds       : bond        0.04821 (  538)
  hydrogen bonds       : angle       4.73301 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7824 (mmp) cc_final: 0.7116 (tpt)
REVERT: A  368 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8563 (ptt-90)
REVERT: B  100 ASN cc_start: 0.9101 (t0) cc_final: 0.8875 (t0)
REVERT: B  111 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8488 (ttm110)
REVERT: B  142 TRP cc_start: 0.8655 (m100) cc_final: 0.8004 (m100)
REVERT: B  143 ARG cc_start: 0.9263 (tmm-80) cc_final: 0.8977 (tmm-80)
REVERT: B  146 TYR cc_start: 0.9269 (t80) cc_final: 0.8666 (t80)
REVERT: B  170 PHE cc_start: 0.8773 (t80) cc_final: 0.8090 (t80)
REVERT: B  172 GLN cc_start: 0.9204 (tt0) cc_final: 0.9003 (tp-100)
REVERT: B  243 ASN cc_start: 0.8822 (p0) cc_final: 0.8539 (p0)
REVERT: B  247 TRP cc_start: 0.9356 (p-90) cc_final: 0.9062 (p-90)
REVERT: B  252 TYR cc_start: 0.8435 (t80) cc_final: 0.8093 (t80)
REVERT: B  258 ARG cc_start: 0.9037 (ttp-170) cc_final: 0.8472 (ttp-110)
REVERT: B  261 ARG cc_start: 0.9198 (tpp80) cc_final: 0.8929 (tpp80)
REVERT: B  266 ASN cc_start: 0.9379 (m110) cc_final: 0.9081 (m-40)
REVERT: C  187 MET cc_start: 0.8364 (mmm) cc_final: 0.7749 (mmm)
REVERT: C  381 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8326 (mm-30)
REVERT: D  100 ASN cc_start: 0.8699 (t0) cc_final: 0.8399 (t0)
REVERT: D  106 MET cc_start: 0.8555 (tpp) cc_final: 0.8300 (tpp)
REVERT: D  170 PHE cc_start: 0.9080 (t80) cc_final: 0.8849 (t80)
REVERT: D  171 PHE cc_start: 0.9235 (m-80) cc_final: 0.8998 (m-10)
REVERT: D  243 ASN cc_start: 0.8747 (p0) cc_final: 0.8385 (p0)
REVERT: D  258 ARG cc_start: 0.9043 (ttm170) cc_final: 0.8332 (mtm180)
REVERT: D  266 ASN cc_start: 0.9344 (m110) cc_final: 0.8995 (m110)
REVERT: D  270 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8068 (pp)
  outliers start: 25
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1099
  time to fit residues: 22.4596
Evaluate side-chains
  143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 37 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 226 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.048609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.033461 restraints weight = 37053.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2483 rms_B_bonded: 3.85
r_work: 0.2306 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8198  Z= 0.139
  Angle     :  0.609   7.454  11081  Z= 0.323
  Chirality :  0.041   0.175   1312
  Planarity :  0.004   0.055   1423
  Dihedral  :  5.125  43.273   1115
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.87 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.15 (0.28), residues: 1036
  helix:  2.44 (0.21), residues: 658
  sheet: -1.47 (0.46), residues: 132
  loop : -2.78 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 395 
 TYR   0.019   0.001   TYR D 252 
 PHE   0.021   0.001   PHE B 171 
 TRP   0.017   0.002   TRP D 247 
 HIS   0.009   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8198)
  covalent geometry    : angle       0.60948 (11081)
  hydrogen bonds       : bond        0.04735 (  538)
  hydrogen bonds       : angle       4.56861 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7730 (mmp) cc_final: 0.6955 (tpp)
REVERT: A  368 ARG cc_start: 0.9082 (mtm110) cc_final: 0.8547 (ptt-90)
REVERT: B  100 ASN cc_start: 0.9091 (t0) cc_final: 0.8880 (t0)
REVERT: B  106 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7937 (ptm)
REVERT: B  111 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8690 (ttm110)
REVERT: B  131 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.7856 (p)
REVERT: B  142 TRP cc_start: 0.8683 (m100) cc_final: 0.7997 (m100)
REVERT: B  143 ARG cc_start: 0.9255 (tmm-80) cc_final: 0.8845 (tmm-80)
REVERT: B  243 ASN cc_start: 0.8789 (p0) cc_final: 0.8469 (p0)
REVERT: B  247 TRP cc_start: 0.9337 (p-90) cc_final: 0.9068 (p-90)
REVERT: B  252 TYR cc_start: 0.8426 (t80) cc_final: 0.8188 (t80)
REVERT: B  258 ARG cc_start: 0.8981 (ttp-170) cc_final: 0.8550 (ttp-110)
REVERT: B  261 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8960 (tpp80)
REVERT: B  266 ASN cc_start: 0.9346 (m110) cc_final: 0.9059 (m110)
REVERT: C  381 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8357 (mm-30)
REVERT: D  100 ASN cc_start: 0.8702 (t0) cc_final: 0.8347 (t0)
REVERT: D  106 MET cc_start: 0.8473 (tpp) cc_final: 0.8109 (ttm)
REVERT: D  111 ARG cc_start: 0.9181 (ttm110) cc_final: 0.8461 (ttm110)
REVERT: D  171 PHE cc_start: 0.9253 (m-80) cc_final: 0.8936 (m-10)
REVERT: D  172 GLN cc_start: 0.9268 (tt0) cc_final: 0.9018 (tp-100)
REVERT: D  243 ASN cc_start: 0.8704 (p0) cc_final: 0.8340 (p0)
REVERT: D  252 TYR cc_start: 0.8340 (t80) cc_final: 0.8131 (t80)
REVERT: D  258 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8276 (mtm180)
REVERT: D  266 ASN cc_start: 0.9341 (m110) cc_final: 0.9026 (m110)
  outliers start: 29
  outliers final: 19
  residues processed: 156
  average time/residue: 0.1028
  time to fit residues: 21.1960
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  269 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 80 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   chunk 41 optimal weight:   10.0000
   chunk 32 optimal weight:    0.1980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0050
   chunk 58 optimal weight:    3.9990
   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 357 ASN
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** 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 = 0.3106 r_free = 0.3106 target = 0.060860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.046046 restraints weight = 36595.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2557 rms_B_bonded: 3.83
r_work: 0.2380 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8198  Z= 0.119
  Angle     :  0.616   8.462  11081  Z= 0.323
  Chirality :  0.040   0.167   1312
  Planarity :  0.004   0.059   1423
  Dihedral  :  4.722  32.392   1114
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.33 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.50 (0.28), residues: 1036
  helix:  2.65 (0.21), residues: 658
  sheet: -1.20 (0.47), residues: 132
  loop : -2.51 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 395 
 TYR   0.013   0.001   TYR B 205 
 PHE   0.011   0.001   PHE B 170 
 TRP   0.021   0.001   TRP D 247 
 HIS   0.009   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8198)
  covalent geometry    : angle       0.61593 (11081)
  hydrogen bonds       : bond        0.03612 (  538)
  hydrogen bonds       : angle       4.31773 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7710 (mmp) cc_final: 0.7393 (tpp)
REVERT: A  381 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8308 (mm-30)
REVERT: B  100 ASN cc_start: 0.9106 (t0) cc_final: 0.8897 (t0)
REVERT: B  142 TRP cc_start: 0.8646 (m100) cc_final: 0.7768 (m100)
REVERT: B  143 ARG cc_start: 0.9165 (tmm-80) cc_final: 0.8682 (tmm-80)
REVERT: B  243 ASN cc_start: 0.8712 (p0) cc_final: 0.8437 (p0)
REVERT: B  247 TRP cc_start: 0.9281 (p-90) cc_final: 0.9051 (p-90)
REVERT: B  258 ARG cc_start: 0.9024 (ttp-170) cc_final: 0.8496 (ttp-110)
REVERT: B  261 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8941 (tpp80)
REVERT: B  266 ASN cc_start: 0.9361 (m110) cc_final: 0.9075 (m110)
REVERT: C  187 MET cc_start: 0.7377 (tpp) cc_final: 0.6859 (tpp)
REVERT: C  381 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8366 (mm-30)
REVERT: D  100 ASN cc_start: 0.8704 (t0) cc_final: 0.8300 (t0)
REVERT: D  106 MET cc_start: 0.8420 (tpp) cc_final: 0.8028 (ttm)
REVERT: D  111 ARG cc_start: 0.9163 (ttm110) cc_final: 0.8536 (ttm110)
REVERT: D  142 TRP cc_start: 0.8405 (m100) cc_final: 0.6237 (m100)
REVERT: D  171 PHE cc_start: 0.9229 (m-80) cc_final: 0.8824 (m-10)
REVERT: D  225 ASP cc_start: 0.8468 (p0) cc_final: 0.8255 (p0)
REVERT: D  228 MET cc_start: 0.9117 (tpp) cc_final: 0.8676 (tpp)
REVERT: D  229 ASN cc_start: 0.9040 (t0) cc_final: 0.8698 (t0)
REVERT: D  243 ASN cc_start: 0.8600 (p0) cc_final: 0.8214 (p0)
REVERT: D  258 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8557 (mtm180)
REVERT: D  266 ASN cc_start: 0.9340 (m110) cc_final: 0.9028 (m110)
REVERT: D  268 PHE cc_start: 0.8906 (m-80) cc_final: 0.8558 (m-80)
  outliers start: 30
  outliers final: 16
  residues processed: 149
  average time/residue: 0.0994
  time to fit residues: 19.6108
Evaluate side-chains
  139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  234 ASN
Chi-restraints excluded: chain D residue  269 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 87 optimal weight:   30.0000
   chunk 89 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 37 optimal weight:   30.0000
   chunk 33 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 115 HIS ** 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 = 0.2965 r_free = 0.2965 target = 0.046437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2397 r_free = 0.2397 target = 0.031885 restraints weight = 37299.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.2430 rms_B_bonded: 3.54
r_work: 0.2257 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8991
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8198  Z= 0.237
  Angle     :  0.684   8.534  11081  Z= 0.361
  Chirality :  0.043   0.239   1312
  Planarity :  0.005   0.064   1423
  Dihedral  :  4.885  35.730   1112
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.82 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.40 (0.28), residues: 1036
  helix:  2.46 (0.20), residues: 656
  sheet: -1.08 (0.48), residues: 134
  loop : -2.28 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 201 
 TYR   0.018   0.002   TYR D 252 
 PHE   0.022   0.001   PHE D 164 
 TRP   0.021   0.002   TRP D 247 
 HIS   0.011   0.002   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 8198)
  covalent geometry    : angle       0.68384 (11081)
  hydrogen bonds       : bond        0.06448 (  538)
  hydrogen bonds       : angle       4.66959 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7838 (mmp) cc_final: 0.7617 (tpp)
REVERT: A  381 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8340 (mm-30)
REVERT: B  100 ASN cc_start: 0.9071 (t0) cc_final: 0.8853 (t0)
REVERT: B  142 TRP cc_start: 0.8721 (m100) cc_final: 0.8393 (m100)
REVERT: B  143 ARG cc_start: 0.9188 (tmm-80) cc_final: 0.8742 (tmm-80)
REVERT: B  243 ASN cc_start: 0.8673 (p0) cc_final: 0.8383 (p0)
REVERT: B  247 TRP cc_start: 0.9320 (p-90) cc_final: 0.9097 (p-90)
REVERT: B  252 TYR cc_start: 0.8318 (t80) cc_final: 0.8093 (t80)
REVERT: B  261 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8915 (tpp80)
REVERT: B  266 ASN cc_start: 0.9306 (m110) cc_final: 0.9027 (m110)
REVERT: C  187 MET cc_start: 0.7302 (tpp) cc_final: 0.6813 (tpp)
REVERT: C  381 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8350 (mm-30)
REVERT: D  100 ASN cc_start: 0.8820 (t0) cc_final: 0.8478 (t0)
REVERT: D  106 MET cc_start: 0.8350 (tpp) cc_final: 0.8112 (ttm)
REVERT: D  111 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8559 (ttm110)
REVERT: D  171 PHE cc_start: 0.9172 (m-80) cc_final: 0.8854 (m-10)
REVERT: D  178 GLU cc_start: 0.9409 (pt0) cc_final: 0.9088 (mp0)
REVERT: D  205 TYR cc_start: 0.8974 (p90) cc_final: 0.8707 (p90)
REVERT: D  243 ASN cc_start: 0.8608 (p0) cc_final: 0.8223 (p0)
REVERT: D  258 ARG cc_start: 0.8977 (ttm170) cc_final: 0.8417 (mtm180)
REVERT: D  266 ASN cc_start: 0.9265 (m110) cc_final: 0.8932 (m110)
REVERT: D  270 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8882 (pp)
  outliers start: 20
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1071
  time to fit residues: 20.0704
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 95 optimal weight:   30.0000
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.048322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.033936 restraints weight = 36778.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.2506 rms_B_bonded: 3.57
r_work: 0.2338 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8198  Z= 0.133
  Angle     :  0.646   8.984  11081  Z= 0.336
  Chirality :  0.041   0.214   1312
  Planarity :  0.004   0.065   1423
  Dihedral  :  4.695  35.217   1112
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.84 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.66 (0.28), residues: 1036
  helix:  2.65 (0.21), residues: 658
  sheet: -0.79 (0.49), residues: 132
  loop : -2.32 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 395 
 TYR   0.018   0.001   TYR D 252 
 PHE   0.016   0.001   PHE D 170 
 TRP   0.025   0.002   TRP D 247 
 HIS   0.011   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8198)
  covalent geometry    : angle       0.64623 (11081)
  hydrogen bonds       : bond        0.04472 (  538)
  hydrogen bonds       : angle       4.37428 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7829 (mmp) cc_final: 0.7618 (tpp)
REVERT: A  381 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8342 (mm-30)
REVERT: B  129 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8343 (mm-30)
REVERT: B  142 TRP cc_start: 0.8597 (m100) cc_final: 0.7880 (m100)
REVERT: B  143 ARG cc_start: 0.9128 (tmm-80) cc_final: 0.8647 (tmm-80)
REVERT: B  205 TYR cc_start: 0.9083 (p90) cc_final: 0.8843 (p90)
REVERT: B  243 ASN cc_start: 0.8649 (p0) cc_final: 0.8378 (p0)
REVERT: B  252 TYR cc_start: 0.8286 (t80) cc_final: 0.8069 (t80)
REVERT: B  258 ARG cc_start: 0.8937 (ttp-110) cc_final: 0.8335 (ttp-110)
REVERT: B  266 ASN cc_start: 0.9335 (m110) cc_final: 0.9049 (m110)
REVERT: C  187 MET cc_start: 0.7054 (tpp) cc_final: 0.6610 (tpp)
REVERT: C  381 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8389 (mm-30)
REVERT: D  100 ASN cc_start: 0.8755 (t0) cc_final: 0.8330 (t0)
REVERT: D  106 MET cc_start: 0.8410 (tpp) cc_final: 0.7984 (ttm)
REVERT: D  111 ARG cc_start: 0.9131 (ttm110) cc_final: 0.8652 (ttm110)
REVERT: D  142 TRP cc_start: 0.8470 (m100) cc_final: 0.6066 (m100)
REVERT: D  178 GLU cc_start: 0.9391 (pt0) cc_final: 0.9035 (mp0)
REVERT: D  243 ASN cc_start: 0.8594 (p0) cc_final: 0.8230 (p0)
REVERT: D  258 ARG cc_start: 0.8933 (ttm170) cc_final: 0.8661 (mtm180)
REVERT: D  266 ASN cc_start: 0.9294 (m110) cc_final: 0.8953 (m110)
REVERT: D  268 PHE cc_start: 0.8974 (m-80) cc_final: 0.8593 (m-80)
REVERT: D  270 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.7532 (pp)
  outliers start: 20
  outliers final: 18
  residues processed: 139
  average time/residue: 0.1067
  time to fit residues: 19.5737
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0870
   chunk 24 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0030
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.3772

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** 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 = 0.3044 r_free = 0.3044 target = 0.049171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2499 r_free = 0.2499 target = 0.034617 restraints weight = 37003.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2529 rms_B_bonded: 3.62
r_work: 0.2367 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8198  Z= 0.126
  Angle     :  0.670  16.934  11081  Z= 0.338
  Chirality :  0.040   0.147   1312
  Planarity :  0.004   0.064   1423
  Dihedral  :  4.572  34.285   1111
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.97 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.73 (0.28), residues: 1036
  helix:  2.71 (0.21), residues: 658
  sheet: -0.87 (0.49), residues: 134
  loop : -2.25 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 261 
 TYR   0.017   0.001   TYR D 252 
 PHE   0.028   0.001   PHE D 164 
 TRP   0.020   0.002   TRP D 247 
 HIS   0.011   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8198)
  covalent geometry    : angle       0.67019 (11081)
  hydrogen bonds       : bond        0.04060 (  538)
  hydrogen bonds       : angle       4.28090 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.7792 (mmp) cc_final: 0.7572 (tpp)
REVERT: A  381 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8354 (mm-30)
REVERT: B  111 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8870 (ttm110)
REVERT: B  129 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8407 (mm-30)
REVERT: B  143 ARG cc_start: 0.9135 (tmm-80) cc_final: 0.8872 (tmm-80)
REVERT: B  243 ASN cc_start: 0.8650 (p0) cc_final: 0.8376 (p0)
REVERT: B  261 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8904 (tpp80)
REVERT: B  266 ASN cc_start: 0.9337 (m110) cc_final: 0.9049 (m110)
REVERT: C  187 MET cc_start: 0.6905 (tpp) cc_final: 0.6493 (tpp)
REVERT: C  318 LEU cc_start: 0.9082 (pt) cc_final: 0.8873 (pt)
REVERT: C  381 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8402 (mm-30)
REVERT: D   99 MET cc_start: 0.8978 (mmm) cc_final: 0.8768 (mmm)
REVERT: D  100 ASN cc_start: 0.8693 (t0) cc_final: 0.8260 (t0)
REVERT: D  142 TRP cc_start: 0.8423 (m100) cc_final: 0.6310 (m100)
REVERT: D  178 GLU cc_start: 0.9417 (pt0) cc_final: 0.9025 (mp0)
REVERT: D  205 TYR cc_start: 0.8974 (p90) cc_final: 0.8766 (p90)
REVERT: D  243 ASN cc_start: 0.8594 (p0) cc_final: 0.8233 (p0)
REVERT: D  258 ARG cc_start: 0.8930 (ttm170) cc_final: 0.8545 (mtm180)
REVERT: D  266 ASN cc_start: 0.9295 (m110) cc_final: 0.8950 (m110)
REVERT: D  268 PHE cc_start: 0.8894 (m-80) cc_final: 0.8578 (m-80)
REVERT: D  270 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.7894 (pp)
  outliers start: 20
  outliers final: 16
  residues processed: 140
  average time/residue: 0.1004
  time to fit residues: 18.7649
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 49 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 45 optimal weight:   30.0000
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** 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 = 0.3039 r_free = 0.3039 target = 0.049166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2496 r_free = 0.2496 target = 0.034663 restraints weight = 36882.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2524 rms_B_bonded: 3.59
r_work: 0.2358 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8198  Z= 0.133
  Angle     :  0.666  12.473  11081  Z= 0.342
  Chirality :  0.041   0.174   1312
  Planarity :  0.004   0.060   1423
  Dihedral  :  4.524  34.055   1111
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.54 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.75 (0.28), residues: 1036
  helix:  2.71 (0.21), residues: 660
  sheet: -0.87 (0.48), residues: 134
  loop : -2.20 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 261 
 TYR   0.014   0.001   TYR D 252 
 PHE   0.020   0.001   PHE D 171 
 TRP   0.016   0.002   TRP B 247 
 HIS   0.011   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8198)
  covalent geometry    : angle       0.66637 (11081)
  hydrogen bonds       : bond        0.04373 (  538)
  hydrogen bonds       : angle       4.27482 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8360 (mm-30)
REVERT: B  111 ARG cc_start: 0.9069 (ttm110) cc_final: 0.8866 (ttm110)
REVERT: B  129 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: B  143 ARG cc_start: 0.9124 (tmm-80) cc_final: 0.8880 (tmm-80)
REVERT: B  205 TYR cc_start: 0.8967 (p90) cc_final: 0.8722 (p90)
REVERT: B  243 ASN cc_start: 0.8675 (p0) cc_final: 0.8398 (p0)
REVERT: B  261 ARG cc_start: 0.9088 (tpp80) cc_final: 0.8886 (tpp80)
REVERT: B  266 ASN cc_start: 0.9337 (m110) cc_final: 0.9049 (m110)
REVERT: C  187 MET cc_start: 0.6804 (tpp) cc_final: 0.6411 (tpp)
REVERT: C  318 LEU cc_start: 0.9080 (pt) cc_final: 0.8850 (pt)
REVERT: C  381 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8402 (mm-30)
REVERT: D   99 MET cc_start: 0.9048 (mmm) cc_final: 0.8678 (mmm)
REVERT: D  100 ASN cc_start: 0.8715 (t0) cc_final: 0.8249 (t0)
REVERT: D  178 GLU cc_start: 0.9386 (pt0) cc_final: 0.8950 (mp0)
REVERT: D  205 TYR cc_start: 0.8920 (p90) cc_final: 0.8715 (p90)
REVERT: D  243 ASN cc_start: 0.8592 (p0) cc_final: 0.8241 (p0)
REVERT: D  258 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8650 (ttp-170)
REVERT: D  266 ASN cc_start: 0.9272 (m110) cc_final: 0.8938 (m110)
REVERT: D  270 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8718 (pp)
  outliers start: 20
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0985
  time to fit residues: 18.0236
Evaluate side-chains
  136 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 76 optimal weight:    0.1980
   chunk 69 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** 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 = 0.3043 r_free = 0.3043 target = 0.049290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2496 r_free = 0.2496 target = 0.034662 restraints weight = 36715.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.2525 rms_B_bonded: 3.62
r_work: 0.2359 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8928
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8198  Z= 0.137
  Angle     :  0.681  12.382  11081  Z= 0.351
  Chirality :  0.041   0.166   1312
  Planarity :  0.004   0.059   1423
  Dihedral  :  4.576  34.517   1111
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.10 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 (0.28), residues: 1036
  helix:  2.75 (0.21), residues: 658
  sheet: -0.85 (0.47), residues: 134
  loop : -2.18 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 258 
 TYR   0.015   0.001   TYR D 252 
 PHE   0.033   0.001   PHE D 164 
 TRP   0.015   0.002   TRP B 247 
 HIS   0.011   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8198)
  covalent geometry    : angle       0.68090 (11081)
  hydrogen bonds       : bond        0.04358 (  538)
  hydrogen bonds       : angle       4.26501 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8371 (mm-30)
REVERT: B  129 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8383 (mm-30)
REVERT: B  143 ARG cc_start: 0.9148 (tmm-80) cc_final: 0.8925 (tmm-80)
REVERT: B  205 TYR cc_start: 0.8944 (p90) cc_final: 0.8701 (p90)
REVERT: B  243 ASN cc_start: 0.8666 (p0) cc_final: 0.8382 (p0)
REVERT: B  266 ASN cc_start: 0.9346 (m110) cc_final: 0.9066 (m110)
REVERT: C  187 MET cc_start: 0.6738 (tpp) cc_final: 0.6344 (tpp)
REVERT: C  318 LEU cc_start: 0.9102 (pt) cc_final: 0.8860 (pt)
REVERT: D   99 MET cc_start: 0.9084 (mmm) cc_final: 0.8710 (mmm)
REVERT: D  100 ASN cc_start: 0.8691 (t0) cc_final: 0.8263 (t0)
REVERT: D  106 MET cc_start: 0.8583 (tmm) cc_final: 0.8015 (ppp)
REVERT: D  111 ARG cc_start: 0.9312 (ttm110) cc_final: 0.8854 (ttm110)
REVERT: D  178 GLU cc_start: 0.9373 (pt0) cc_final: 0.8940 (mp0)
REVERT: D  243 ASN cc_start: 0.8595 (p0) cc_final: 0.8255 (p0)
REVERT: D  258 ARG cc_start: 0.8917 (ttm170) cc_final: 0.8703 (ttp-170)
REVERT: D  266 ASN cc_start: 0.9281 (m110) cc_final: 0.8940 (m110)
REVERT: D  268 PHE cc_start: 0.8895 (m-80) cc_final: 0.8593 (m-80)
REVERT: D  270 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8890 (pp)
  outliers start: 18
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1014
  time to fit residues: 18.2734
Evaluate side-chains
  134 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 357 ASN
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.046585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2407 r_free = 0.2407 target = 0.032211 restraints weight = 37097.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2438 rms_B_bonded: 3.46
r_work: 0.2266 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8983
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   8198  Z= 0.259
  Angle     :  0.766  11.634  11081  Z= 0.399
  Chirality :  0.044   0.206   1312
  Planarity :  0.005   0.058   1423
  Dihedral  :  4.899  38.240   1111
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.67 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.44 (0.28), residues: 1036
  helix:  2.44 (0.20), residues: 660
  sheet: -0.96 (0.47), residues: 134
  loop : -2.25 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 258 
 TYR   0.023   0.002   TYR D 252 
 PHE   0.023   0.002   PHE B 170 
 TRP   0.012   0.002   TRP B 247 
 HIS   0.010   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 ( 8198)
  covalent geometry    : angle       0.76601 (11081)
  hydrogen bonds       : bond        0.06600 (  538)
  hydrogen bonds       : angle       4.65433 ( 1563)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  381 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: B  129 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8492 (mm-30)
REVERT: B  243 ASN cc_start: 0.8642 (p0) cc_final: 0.8376 (p0)
REVERT: B  258 ARG cc_start: 0.8939 (ttp-170) cc_final: 0.8469 (mtm180)
REVERT: B  266 ASN cc_start: 0.9327 (m110) cc_final: 0.9059 (m110)
REVERT: B  270 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.7741 (pp)
REVERT: C  187 MET cc_start: 0.6856 (tpp) cc_final: 0.6484 (tpp)
REVERT: C  275 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8365 (ttt180)
REVERT: C  318 LEU cc_start: 0.9117 (pt) cc_final: 0.8875 (pt)
REVERT: D   99 MET cc_start: 0.9184 (mmm) cc_final: 0.8874 (mmm)
REVERT: D  100 ASN cc_start: 0.8761 (t0) cc_final: 0.8368 (t0)
REVERT: D  106 MET cc_start: 0.8551 (tmm) cc_final: 0.7490 (ppp)
REVERT: D  111 ARG cc_start: 0.9246 (ttm110) cc_final: 0.8811 (ttm110)
REVERT: D  178 GLU cc_start: 0.9358 (pt0) cc_final: 0.8907 (mp0)
REVERT: D  243 ASN cc_start: 0.8625 (p0) cc_final: 0.8274 (p0)
REVERT: D  258 ARG cc_start: 0.8941 (ttm170) cc_final: 0.8710 (ttp-170)
REVERT: D  266 ASN cc_start: 0.9240 (m110) cc_final: 0.8955 (m-40)
REVERT: D  270 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8741 (pp)
  outliers start: 17
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1070
  time to fit residues: 19.0192
Evaluate side-chains
  133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  215 SER
Chi-restraints excluded: chain C residue  243 LYS
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  270 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.048502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2474 r_free = 0.2474 target = 0.033949 restraints weight = 36755.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2507 rms_B_bonded: 3.55
r_work: 0.2339 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8938
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8198  Z= 0.149
  Angle     :  0.736  12.224  11081  Z= 0.381
  Chirality :  0.042   0.162   1312
  Planarity :  0.004   0.058   1423
  Dihedral  :  4.723  36.533   1111
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.56 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.66 (0.28), residues: 1036
  helix:  2.63 (0.20), residues: 660
  sheet: -0.90 (0.48), residues: 134
  loop : -2.22 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 111 
 TYR   0.019   0.001   TYR D 252 
 PHE   0.013   0.001   PHE D 164 
 TRP   0.016   0.002   TRP B 247 
 HIS   0.010   0.001   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8198)
  covalent geometry    : angle       0.73567 (11081)
  hydrogen bonds       : bond        0.04631 (  538)
  hydrogen bonds       : angle       4.39005 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1669.55 seconds
wall clock time: 29 minutes 27.62 seconds (1767.62 seconds total)