Starting phenix.real_space_refine
on Fri Aug 22 19:01:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iq4_35657/08_2025/8iq4_35657.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.101
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4555      2.51       5
     N    1208      2.21       5
     O    1265      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7080
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2065
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 63
    Chain: "A"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1564
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 3, 'TRANS': 197}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 78
    Chain: "B"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2342
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 6, 'GLU:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 13, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 142
    Chain: "G"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 238
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "N"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 845
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'87Q': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.68, per 1000 atoms: 0.24
  Number of scatterers: 7080
  At special positions: 0
  Unit cell: (70.2656, 96.6152, 124.063, 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      52     16.00
     O    1265      8.00
     N    1208      7.00
     C    4555      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 415.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 11 sheets defined
      40.9% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 29 through 60
      removed outlier: 4.471A  pdb=" N   SER R  33 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 94
    Processing helix  chain 'R' and resid 105 through 139
      Proline residue:  R 122  - end of helix
    Processing helix  chain 'R' and resid 139 through 146
    Processing helix  chain 'R' and resid 147 through 173
      removed outlier: 4.164A  pdb=" N   HIS R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL R 152 " --> pdb=" O   THR R 148 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 195 through 229
      removed outlier: 4.018A  pdb=" N   ARG R 199 " --> pdb=" O   ASP R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 275
      Proline residue:  R 264  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.826A  pdb=" N   PHE R 288 " --> pdb=" O   GLU R 284 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 313
    Processing helix  chain 'A' and resid 18 through 39
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.532A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 3.759A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 392
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 16 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 179
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.721A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.472A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.746A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.039A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.153A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.450A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.550A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.575A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.529A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1173 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: 1.20

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2261
        1.34 -     1.46: 1812
        1.46 -     1.58: 3078
        1.58 -     1.70: 0
        1.70 -     1.82: 71
  Bond restraints: 7222
  Sorted by residual:
  bond pdb=" C13 87Q R 401 "
       pdb=" C14 87Q R 401 "
    ideal  model  delta    sigma   weight residual
    1.499  1.563 -0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" C10 87Q R 401 "
       pdb=" C11 87Q R 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.540 -0.050 2.00e-02 2.50e+03 6.19e+00
  bond pdb=" C15 87Q R 401 "
       pdb=" C16 87Q R 401 "
    ideal  model  delta    sigma   weight residual
    1.500  1.546 -0.046 2.00e-02 2.50e+03 5.23e+00
  bond pdb=" C06 87Q R 401 "
       pdb=" C09 87Q R 401 "
    ideal  model  delta    sigma   weight residual
    1.505  1.542 -0.037 2.00e-02 2.50e+03 3.34e+00
  bond pdb=" C06 87Q R 401 "
       pdb=" O08 87Q R 401 "
    ideal  model  delta    sigma   weight residual
    1.426  1.391  0.035 2.00e-02 2.50e+03 3.08e+00
  ... (remaining 7217 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.18: 9818
        5.18 -    10.36: 6
       10.36 -    15.55: 2
       15.55 -    20.73: 0
       20.73 -    25.91: 1
  Bond angle restraints: 9827
  Sorted by residual:
  angle pdb=" C09 87Q R 401 "
        pdb=" C10 87Q R 401 "
        pdb=" C11 87Q R 401 "
      ideal   model   delta    sigma   weight residual
     124.44  150.35  -25.91 3.00e+00 1.11e-01 7.46e+01
  angle pdb=" C13 87Q R 401 "
        pdb=" C14 87Q R 401 "
        pdb=" C15 87Q R 401 "
      ideal   model   delta    sigma   weight residual
     126.67  114.18   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" C06 87Q R 401 "
        pdb=" C09 87Q R 401 "
        pdb=" C10 87Q R 401 "
      ideal   model   delta    sigma   weight residual
     127.22  114.91   12.31 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" C   ARG R  59 "
        pdb=" N   GLN R  60 "
        pdb=" CA  GLN R  60 "
      ideal   model   delta    sigma   weight residual
     122.31  115.55    6.76 1.81e+00 3.05e-01 1.40e+01
  angle pdb=" C14 87Q R 401 "
        pdb=" C15 87Q R 401 "
        pdb=" C16 87Q R 401 "
      ideal   model   delta    sigma   weight residual
     126.41  117.48    8.93 3.00e+00 1.11e-01 8.86e+00
  ... (remaining 9822 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3777
       17.81 -    35.62: 337
       35.62 -    53.44: 83
       53.44 -    71.25: 17
       71.25 -    89.06: 5
  Dihedral angle restraints: 4219
    sinusoidal: 1453
      harmonic: 2766
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.49   35.49     1      1.00e+01 1.00e-02 1.78e+01
  dihedral pdb=" CA  ARG R 100 "
           pdb=" C   ARG R 100 "
           pdb=" N   PHE R 101 "
           pdb=" CA  PHE R 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.08   20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" SG  CYS N  99 "
           pdb=" CB  CYS N 107 "
           pdb=" SG  CYS N 107 "
           pdb=" CA  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -1.88  -71.12     1      2.00e+01 2.50e-03 1.62e+01
  ... (remaining 4216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1098
       0.082 -    0.163: 68
       0.163 -    0.244: 2
       0.244 -    0.326: 1
       0.326 -    0.407: 1
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" C12 87Q R 401 "
            pdb=" C11 87Q R 401 "
            pdb=" C13 87Q R 401 "
            pdb=" C22 87Q R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.94    0.41 2.00e-01 2.50e+01 4.15e+00
  chirality pdb=" C11 87Q R 401 "
            pdb=" C10 87Q R 401 "
            pdb=" C12 87Q R 401 "
            pdb=" C25 87Q R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.92   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" C06 87Q R 401 "
            pdb=" C05 87Q R 401 "
            pdb=" C07 87Q R 401 "
            pdb=" C09 87Q R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.75    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 263 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO R 264 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO R 264 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 264 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO B 236 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.61e+00
        pdb=" C   THR B  87 "    0.028 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 945
        2.75 -     3.29: 6525
        3.29 -     3.83: 11972
        3.83 -     4.36: 14102
        4.36 -     4.90: 25373
  Nonbonded interactions: 58917
  Sorted by model distance:
  nonbonded pdb=" O   SER N 112 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.269 3.040
  ... (remaining 58912 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
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      :  0.003   0.064   7225  Z= 0.144
  Angle     :  0.603  25.912   9833  Z= 0.294
  Chirality :  0.043   0.407   1170
  Planarity :  0.003   0.047   1225
  Dihedral  : 14.910  89.058   2416
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 12.77 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.27), residues: 930
  helix:  3.05 (0.26), residues: 340
  sheet:  1.05 (0.35), residues: 206
  loop : -1.16 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.019   0.001   PHE R 165 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7222)
  covalent geometry    : angle       0.60317 ( 9827)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.82818 (    6)
  hydrogen bonds       : bond        0.12238 (  409)
  hydrogen bonds       : angle       4.98957 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.320 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 99
  average time/residue: 0.5537
  time to fit residues: 57.9451
Evaluate side-chains
  98 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain A residue  365 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 296 ASN
B 175 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.137603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.113513 restraints weight = 7808.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.43
r_work: 0.3196 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.0635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7225  Z= 0.140
  Angle     :  0.500   6.464   9833  Z= 0.278
  Chirality :  0.041   0.153   1170
  Planarity :  0.004   0.049   1225
  Dihedral  :  5.992  88.655   1052
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.48 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.27), residues: 930
  helix:  3.09 (0.26), residues: 344
  sheet:  1.09 (0.34), residues: 209
  loop : -1.17 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 231 
 TYR   0.013   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 101 
 TRP   0.014   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7222)
  covalent geometry    : angle       0.49927 ( 9827)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       0.86239 (    6)
  hydrogen bonds       : bond        0.05036 (  409)
  hydrogen bonds       : angle       4.45499 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B  219 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7711 (mtp180)
REVERT: B  234 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8356 (t80)
REVERT: N   95 TYR cc_start: 0.8725 (m-80) cc_final: 0.8493 (m-80)
  outliers start: 15
  outliers final: 7
  residues processed: 109
  average time/residue: 0.4652
  time to fit residues: 53.9392
Evaluate side-chains
  107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** B 237 ASN ** 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 = 0.3588 r_free = 0.3588 target = 0.138240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.114300 restraints weight = 7792.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.43
r_work: 0.3196 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.0756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7225  Z= 0.130
  Angle     :  0.493   8.027   9833  Z= 0.271
  Chirality :  0.041   0.147   1170
  Planarity :  0.003   0.050   1225
  Dihedral  :  5.719  87.571   1050
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.79 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.27), residues: 930
  helix:  3.21 (0.26), residues: 343
  sheet:  1.11 (0.34), residues: 207
  loop : -1.21 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.015   0.001   PHE R 165 
 TRP   0.012   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7222)
  covalent geometry    : angle       0.49302 ( 9827)
  SS BOND              : bond        0.00295 (    3)
  SS BOND              : angle       0.89234 (    6)
  hydrogen bonds       : bond        0.04834 (  409)
  hydrogen bonds       : angle       4.33390 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.291 
Fit side-chains
REVERT: B  219 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7692 (mtp180)
REVERT: B  234 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8361 (t80)
REVERT: N   95 TYR cc_start: 0.8711 (m-80) cc_final: 0.8447 (m-80)
  outliers start: 16
  outliers final: 9
  residues processed: 112
  average time/residue: 0.4649
  time to fit residues: 55.4525
Evaluate side-chains
  110 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.113457 restraints weight = 7772.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.45
r_work: 0.3183 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.0842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7225  Z= 0.138
  Angle     :  0.494   6.494   9833  Z= 0.275
  Chirality :  0.041   0.152   1170
  Planarity :  0.004   0.050   1225
  Dihedral  :  5.700  87.200   1050
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.93 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.27), residues: 930
  helix:  3.15 (0.26), residues: 344
  sheet:  0.95 (0.33), residues: 214
  loop : -1.20 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.011   0.002   TRP B  63 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7222)
  covalent geometry    : angle       0.49364 ( 9827)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.97193 (    6)
  hydrogen bonds       : bond        0.04942 (  409)
  hydrogen bonds       : angle       4.34638 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  219 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7686 (mtp180)
REVERT: B  234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8427 (t80)
REVERT: N   95 TYR cc_start: 0.8706 (m-80) cc_final: 0.8427 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 111
  average time/residue: 0.4453
  time to fit residues: 52.4662
Evaluate side-chains
  112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    0.0770
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.115469 restraints weight = 7783.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.47
r_work: 0.3218 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7225  Z= 0.112
  Angle     :  0.470   8.743   9833  Z= 0.258
  Chirality :  0.040   0.150   1170
  Planarity :  0.003   0.049   1225
  Dihedral  :  5.447  82.849   1050
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.53 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.27), residues: 930
  helix:  3.27 (0.25), residues: 343
  sheet:  1.06 (0.34), residues: 212
  loop : -1.17 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 118 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7222)
  covalent geometry    : angle       0.46934 ( 9827)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.03704 (    6)
  hydrogen bonds       : bond        0.04442 (  409)
  hydrogen bonds       : angle       4.22484 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B  219 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7680 (mtp180)
REVERT: B  234 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: N   38 ARG cc_start: 0.9005 (ptt180) cc_final: 0.8684 (ptt180)
REVERT: N   95 TYR cc_start: 0.8684 (m-80) cc_final: 0.8449 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 114
  average time/residue: 0.4585
  time to fit residues: 55.4823
Evaluate side-chains
  113 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0060
   chunk 69 optimal weight:    0.1980
   chunk 47 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0870
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.3974

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117583 restraints weight = 7798.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.43
r_work: 0.3245 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7225  Z= 0.100
  Angle     :  0.443   6.207   9833  Z= 0.247
  Chirality :  0.039   0.155   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.260  80.323   1050
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.38 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.27), residues: 930
  helix:  3.28 (0.25), residues: 347
  sheet:  1.12 (0.34), residues: 211
  loop : -1.12 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 118 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 7222)
  covalent geometry    : angle       0.44270 ( 9827)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.94553 (    6)
  hydrogen bonds       : bond        0.04133 (  409)
  hydrogen bonds       : angle       4.11709 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.280 
Fit side-chains
REVERT: R  161 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7906 (mm)
REVERT: B  219 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7678 (mtp180)
REVERT: B  234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8206 (t80)
REVERT: N   95 TYR cc_start: 0.8639 (m-80) cc_final: 0.8393 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 0.4530
  time to fit residues: 57.4271
Evaluate side-chains
  114 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 72 optimal weight:    0.1980
   chunk 34 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.141109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117018 restraints weight = 7825.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.46
r_work: 0.3229 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7225  Z= 0.106
  Angle     :  0.467   9.672   9833  Z= 0.256
  Chirality :  0.040   0.156   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.269  80.411   1050
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.82 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.27), residues: 930
  helix:  3.22 (0.25), residues: 350
  sheet:  1.06 (0.34), residues: 213
  loop : -1.13 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 118 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.015   0.001   PHE R 165 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7222)
  covalent geometry    : angle       0.46661 ( 9827)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       1.05897 (    6)
  hydrogen bonds       : bond        0.04240 (  409)
  hydrogen bonds       : angle       4.12948 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.292 
Fit side-chains
REVERT: R  161 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7928 (mm)
REVERT: B  219 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7688 (mtp180)
REVERT: B  234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8259 (t80)
REVERT: N   95 TYR cc_start: 0.8644 (m-80) cc_final: 0.8389 (m-80)
  outliers start: 16
  outliers final: 9
  residues processed: 114
  average time/residue: 0.4986
  time to fit residues: 60.6013
Evaluate side-chains
  115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0470
   chunk 5 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0060
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.140237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116225 restraints weight = 7832.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.44
r_work: 0.3230 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7225  Z= 0.115
  Angle     :  0.468   6.211   9833  Z= 0.260
  Chirality :  0.040   0.160   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.330  81.392   1050
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.11 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.27), residues: 930
  helix:  3.17 (0.25), residues: 350
  sheet:  1.13 (0.34), residues: 212
  loop : -1.18 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7222)
  covalent geometry    : angle       0.46764 ( 9827)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       1.04732 (    6)
  hydrogen bonds       : bond        0.04420 (  409)
  hydrogen bonds       : angle       4.16638 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.268 
Fit side-chains
REVERT: R  161 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: B  219 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7667 (mtp180)
REVERT: B  234 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: N   38 ARG cc_start: 0.8784 (ptt180) cc_final: 0.8543 (ptt180)
REVERT: N   95 TYR cc_start: 0.8644 (m-80) cc_final: 0.8374 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 114
  average time/residue: 0.4619
  time to fit residues: 56.0259
Evaluate side-chains
  116 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    0.0060
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0570
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6316

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.139893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.115742 restraints weight = 7758.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.46
r_work: 0.3218 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7225  Z= 0.120
  Angle     :  0.485   9.576   9833  Z= 0.264
  Chirality :  0.040   0.159   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.371  82.363   1050
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.11 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.27), residues: 930
  helix:  3.23 (0.25), residues: 346
  sheet:  1.12 (0.34), residues: 212
  loop : -1.19 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 118 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7222)
  covalent geometry    : angle       0.48473 ( 9827)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       0.99818 (    6)
  hydrogen bonds       : bond        0.04481 (  409)
  hydrogen bonds       : angle       4.18943 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.298 
Fit side-chains
REVERT: R  161 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7943 (mm)
REVERT: B  219 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7677 (mtp180)
REVERT: B  234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8328 (t80)
REVERT: N   95 TYR cc_start: 0.8649 (m-80) cc_final: 0.8374 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 112
  average time/residue: 0.4463
  time to fit residues: 52.9877
Evaluate side-chains
  116 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.116024 restraints weight = 7777.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.43
r_work: 0.3224 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7225  Z= 0.118
  Angle     :  0.473   6.204   9833  Z= 0.262
  Chirality :  0.040   0.162   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.371  83.068   1050
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.26 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.27), residues: 930
  helix:  3.20 (0.25), residues: 346
  sheet:  1.11 (0.34), residues: 212
  loop : -1.20 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 118 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.019   0.001   PHE R 165 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7222)
  covalent geometry    : angle       0.47244 ( 9827)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       0.98125 (    6)
  hydrogen bonds       : bond        0.04470 (  409)
  hydrogen bonds       : angle       4.19013 ( 1173)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  219 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7662 (mtp180)
REVERT: B  234 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8315 (t80)
REVERT: N   95 TYR cc_start: 0.8642 (m-80) cc_final: 0.8367 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 110
  average time/residue: 0.4912
  time to fit residues: 57.2199
Evaluate side-chains
  115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  196 TRP
Chi-restraints excluded: chain R residue  260 ILE
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   53 GLN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
N 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.115730 restraints weight = 7720.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.43
r_work: 0.3219 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7225  Z= 0.122
  Angle     :  0.491  10.233   9833  Z= 0.267
  Chirality :  0.040   0.161   1170
  Planarity :  0.003   0.048   1225
  Dihedral  :  5.407  84.234   1050
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.26 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.27), residues: 930
  helix:  3.16 (0.25), residues: 346
  sheet:  1.10 (0.34), residues: 212
  loop : -1.19 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 165 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7222)
  covalent geometry    : angle       0.49033 ( 9827)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.97143 (    6)
  hydrogen bonds       : bond        0.04541 (  409)
  hydrogen bonds       : angle       4.20719 ( 1173)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2399.17 seconds
wall clock time: 41 minutes 40.56 seconds (2500.56 seconds total)