Starting phenix.real_space_refine
on Wed Feb  4 06:59:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9le0_63011/02_2026/9le0_63011.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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      59      5.16       5
     C    5852      2.51       5
     N    1558      2.21       5
     O    1709      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 9178
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1919
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2429
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 13, 'TRANS': 291}
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'OYA': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'OYA:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.88, per 1000 atoms: 0.20
  Number of scatterers: 9178
  At special positions: 0
  Unit cell: (84.032, 123.968, 125.632, 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      59     16.00
     O    1709      8.00
     N    1558      7.00
     C    5852      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 167 " - pdb=" SG  CYS R 187 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 230.4 milliseconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2188

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      39.7% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 96 through 101
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 155
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.263A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.758A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.151A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.795A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 18 through 50
      removed outlier: 4.507A  pdb=" N   VAL R  23 " --> pdb=" O   PRO R  19 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LEU R  24 " --> pdb=" O   GLU R  20 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 51 through 54
    Processing helix  chain 'R' and resid 55 through 86
      removed outlier: 4.025A  pdb=" N   THR R  75 " --> pdb=" O   TYR R  71 " (cutoff:3.500A)
      Proline residue:  R  77  - end of helix
    Processing helix  chain 'R' and resid 92 through 126
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 135 through 163
      Proline residue:  R 156  - end of helix
      removed outlier: 3.937A  pdb=" N   ILE R 161 " --> pdb=" O   LYS R 157 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN R 163 " --> pdb=" O   ILE R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 186
    Processing helix  chain 'R' and resid 190 through 225
      removed outlier: 3.978A  pdb=" N   VAL R 207 " --> pdb=" O   VAL R 203 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR R 208 " --> pdb=" O   ILE R 204 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG R 225 " --> pdb=" O   ARG R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 258
      removed outlier: 3.625A  pdb=" N   MET R 256 " --> pdb=" O   SER R 252 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL R 258 " --> pdb=" O   ILE R 254 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 268 through 278
      removed outlier: 4.075A  pdb=" N   VAL R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU R 275 " --> pdb=" O   GLY R 271 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR R 276 " --> pdb=" O   VAL R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 289
      removed outlier: 3.593A  pdb=" N   LEU R 282 " --> pdb=" O   VAL R 278 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 292 through 308
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 76
      removed outlier: 9.407A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   TYR A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASN A 144 " --> pdb=" O   TYR A 108 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ALA A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ILE A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   HIS A 214 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.377A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.576A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.235A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.643A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.505A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.620A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.584A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11
      removed outlier: 6.242A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.540A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 89 through 91
      removed outlier: 8.242A  pdb=" N   ILE R 172 " --> pdb=" O   GLU R   9 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE R  11 " --> pdb=" O   ILE R 172 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1377 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: 1.50

  Time building geometry restraints manager: 0.63 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: 2958
        1.34 -     1.46: 2134
        1.46 -     1.58: 4190
        1.58 -     1.70: 0
        1.70 -     1.81: 85
  Bond restraints: 9367
  Sorted by residual:
  bond pdb=" N   ILE B 270 "
       pdb=" CA  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 9.50e-03 1.11e+04 1.58e+01
  bond pdb=" N   ALA C   7 "
       pdb=" CA  ALA C   7 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   HIS R   4 "
       pdb=" CA  HIS R   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  bond pdb=" N   GLU B   3 "
       pdb=" CA  GLU B   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" N   THR A   4 "
       pdb=" CA  THR A   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  ... (remaining 9362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 12039
        1.22 -     2.43: 535
        2.43 -     3.65: 91
        3.65 -     4.86: 18
        4.86 -     6.08: 9
  Bond angle restraints: 12692
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.53  108.00    5.53 9.80e-01 1.04e+00 3.18e+01
  angle pdb=" CA  TYR S 223 "
        pdb=" CB  TYR S 223 "
        pdb=" CG  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     113.90  108.93    4.97 1.80e+00 3.09e-01 7.63e+00
  angle pdb=" CG  LYS A  25 "
        pdb=" CD  LYS A  25 "
        pdb=" CE  LYS A  25 "
      ideal   model   delta    sigma   weight residual
     111.30  117.38   -6.08 2.30e+00 1.89e-01 6.99e+00
  angle pdb=" CA  GLN B  17 "
        pdb=" CB  GLN B  17 "
        pdb=" CG  GLN B  17 "
      ideal   model   delta    sigma   weight residual
     114.10  118.89   -4.79 2.00e+00 2.50e-01 5.74e+00
  angle pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
        pdb=" CB  THR B  87 "
      ideal   model   delta    sigma   weight residual
     113.65  110.22    3.43 1.47e+00 4.63e-01 5.46e+00
  ... (remaining 12687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 4869
       17.37 -    34.73: 542
       34.73 -    52.10: 134
       52.10 -    69.46: 40
       69.46 -    86.83: 9
  Dihedral angle restraints: 5594
    sinusoidal: 2203
      harmonic: 3391
  Sorted by residual:
  dihedral pdb=" CA  LEU R 160 "
           pdb=" C   LEU R 160 "
           pdb=" N   ILE R 161 "
           pdb=" CA  ILE R 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.24   21.76     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CB  CYS R  95 "
           pdb=" SG  CYS R  95 "
           pdb=" SG  CYS R 177 "
           pdb=" CB  CYS R 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.39   35.39     1      1.00e+01 1.00e-02 1.77e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 5591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1074
       0.041 -    0.082: 278
       0.082 -    0.124: 90
       0.124 -    0.165: 10
       0.165 -    0.206: 3
  Chirality restraints: 1455
  Sorted by residual:
  chirality pdb=" CA  ILE B 270 "
            pdb=" N   ILE B 270 "
            pdb=" C   ILE B 270 "
            pdb=" CB  ILE B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  THR R  38 "
            pdb=" CA  THR R  38 "
            pdb=" OG1 THR R  38 "
            pdb=" CG2 THR R  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" CA  TYR S 223 "
            pdb=" N   TYR S 223 "
            pdb=" C   TYR S 223 "
            pdb=" CB  TYR S 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 1452 not shown)

  Planarity restraints: 1602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 155 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.78e+00
        pdb=" N   PRO R 156 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO R 156 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 156 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO S 224 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO S  75 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1599 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1549
        2.76 -     3.30: 9203
        3.30 -     3.83: 15652
        3.83 -     4.37: 19056
        4.37 -     4.90: 32903
  Nonbonded interactions: 78363
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  17 "
            pdb=" OE1 GLN B  17 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ASP A 114 "
            pdb=" OD1 ASP A 114 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   ASP S 189 "
            pdb=" OD1 ASP S 189 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ARG S  87 "
            pdb=" OD1 ASP S  90 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   GLN R 163 "
            pdb=" OE1 GLN R 163 "
     model   vdw
     2.342 3.040
  ... (remaining 78358 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:             1.960
  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:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.870
  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:             0.010
  Load rotamer database and sin/cos tables:8.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
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      :  0.004   0.161   9372  Z= 0.249
  Angle     :  0.603   6.080  12700  Z= 0.336
  Chirality :  0.042   0.206   1455
  Planarity :  0.004   0.049   1602
  Dihedral  : 16.226  86.831   3394
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 24.43 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.25), residues: 1151
  helix:  2.01 (0.25), residues: 397
  sheet: -0.56 (0.31), residues: 268
  loop : -0.51 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 237 
 TYR   0.017   0.002   TYR S 223 
 PHE   0.023   0.002   PHE R 175 
 TRP   0.018   0.001   TRP A 133 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9367)
  covalent geometry    : angle       0.60243 (12692)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.77118 (    8)
  hydrogen bonds       : bond        0.11925 (  484)
  hydrogen bonds       : angle       6.03747 ( 1377)
  Misc. bond           : bond        0.16101 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 220
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7235 (mtt-85)
REVERT: B   74 SER cc_start: 0.8445 (t) cc_final: 0.8229 (p)
REVERT: B   76 ASP cc_start: 0.7973 (p0) cc_final: 0.7558 (p0)
REVERT: B  277 SER cc_start: 0.8137 (t) cc_final: 0.7790 (m)
REVERT: B  304 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6922 (mtp180)
REVERT: S  109 ASP cc_start: 0.7089 (m-30) cc_final: 0.6880 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 224
  average time/residue: 0.4811
  time to fit residues: 115.4548
Evaluate side-chains
  199 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   96 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 176 GLN
B 239 ASN
B 268 ASN
S  82 GLN
R  54 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.147275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.129336 restraints weight = 12572.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.83
r_work: 0.3683 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9372  Z= 0.168
  Angle     :  0.580   8.660  12700  Z= 0.304
  Chirality :  0.045   0.218   1455
  Planarity :  0.005   0.048   1602
  Dihedral  :  4.390  22.842   1275
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.97 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.25), residues: 1151
  helix:  2.28 (0.25), residues: 402
  sheet: -0.32 (0.31), residues: 271
  loop : -0.48 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 232 
 TYR   0.018   0.002   TYR S 223 
 PHE   0.019   0.002   PHE R 104 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9367)
  covalent geometry    : angle       0.57967 (12692)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.65278 (    8)
  hydrogen bonds       : bond        0.04365 (  484)
  hydrogen bonds       : angle       4.97229 ( 1377)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 220
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7499 (mmt)
REVERT: B   46 ARG cc_start: 0.7444 (ttm170) cc_final: 0.7147 (ttm170)
REVERT: B  129 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7880 (mtp85)
REVERT: B  277 SER cc_start: 0.8108 (t) cc_final: 0.7863 (m)
REVERT: B  304 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6869 (mtp180)
REVERT: C   42 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6928 (mp0)
REVERT: S   83 MET cc_start: 0.8104 (mtm) cc_final: 0.7855 (mtp)
REVERT: S   85 SER cc_start: 0.8139 (t) cc_final: 0.7705 (p)
REVERT: S  109 ASP cc_start: 0.7497 (m-30) cc_final: 0.7272 (m-30)
REVERT: S  118 THR cc_start: 0.8288 (m) cc_final: 0.8038 (p)
REVERT: S  132 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7375 (m)
REVERT: S  203 THR cc_start: 0.7366 (m) cc_final: 0.6997 (p)
REVERT: S  223 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6414 (t80)
REVERT: R  140 THR cc_start: 0.8127 (p) cc_final: 0.7900 (m)
REVERT: R  293 LYS cc_start: 0.8146 (mttm) cc_final: 0.7914 (mttm)
  outliers start: 39
  outliers final: 9
  residues processed: 239
  average time/residue: 0.4724
  time to fit residues: 121.7007
Evaluate side-chains
  224 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 210
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 176 GLN
C  44 HIS
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
R  54 HIS
** R 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.144255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.126171 restraints weight = 12586.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.84
r_work: 0.3631 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   9372  Z= 0.281
  Angle     :  0.627   8.154  12700  Z= 0.328
  Chirality :  0.048   0.244   1455
  Planarity :  0.005   0.050   1602
  Dihedral  :  4.516  19.056   1274
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 21.96 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1151
  helix:  2.05 (0.25), residues: 402
  sheet: -0.27 (0.31), residues: 269
  loop : -0.63 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.022   0.002   TYR S 223 
 PHE   0.028   0.002   PHE R 104 
 TRP   0.020   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 9367)
  covalent geometry    : angle       0.62707 (12692)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       0.76984 (    8)
  hydrogen bonds       : bond        0.04874 (  484)
  hydrogen bonds       : angle       5.08327 ( 1377)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 205
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  116 ASN cc_start: 0.8114 (t0) cc_final: 0.7800 (m-40)
REVERT: A  148 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7489 (mmt)
REVERT: A  166 GLU cc_start: 0.7535 (mp0) cc_final: 0.7270 (mp0)
REVERT: A  195 ASP cc_start: 0.6504 (t0) cc_final: 0.6260 (t0)
REVERT: A  196 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7862 (tp)
REVERT: A  244 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: B  124 TYR cc_start: 0.8463 (m-80) cc_final: 0.8212 (m-80)
REVERT: B  277 SER cc_start: 0.8128 (t) cc_final: 0.7847 (m)
REVERT: C   42 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6996 (mp0)
REVERT: S    5 VAL cc_start: 0.8370 (t) cc_final: 0.8113 (p)
REVERT: S   85 SER cc_start: 0.8279 (t) cc_final: 0.7877 (p)
REVERT: S  109 ASP cc_start: 0.7410 (m-30) cc_final: 0.7170 (m-30)
REVERT: S  132 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7472 (m)
REVERT: S  223 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6419 (t80)
REVERT: R   34 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7985 (mm)
REVERT: R   83 ILE cc_start: 0.7895 (mm) cc_final: 0.7625 (tp)
REVERT: R  140 THR cc_start: 0.8127 (p) cc_final: 0.7904 (m)
REVERT: R  293 LYS cc_start: 0.8160 (mttm) cc_final: 0.7944 (mttm)
REVERT: R  301 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7559 (ttpt)
  outliers start: 41
  outliers final: 17
  residues processed: 225
  average time/residue: 0.4679
  time to fit residues: 113.4604
Evaluate side-chains
  225 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  180 SER
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  220 ILE
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.0980
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 102 optimal weight:    0.0020
   chunk 92 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
B 176 GLN
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.147840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129990 restraints weight = 12697.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.85
r_work: 0.3702 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9372  Z= 0.129
  Angle     :  0.546   8.915  12700  Z= 0.282
  Chirality :  0.043   0.192   1455
  Planarity :  0.004   0.055   1602
  Dihedral  :  4.229  23.434   1274
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 24.04 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1151
  helix:  2.37 (0.25), residues: 402
  sheet: -0.34 (0.31), residues: 275
  loop : -0.50 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 237 
 TYR   0.013   0.001   TYR S 223 
 PHE   0.022   0.001   PHE A  74 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9367)
  covalent geometry    : angle       0.54566 (12692)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.62167 (    8)
  hydrogen bonds       : bond        0.04048 (  484)
  hydrogen bonds       : angle       4.74975 ( 1377)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 212
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  116 ASN cc_start: 0.8136 (t0) cc_final: 0.7823 (m-40)
REVERT: A  117 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7416 (mtm-85)
REVERT: A  148 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7435 (mmt)
REVERT: A  166 GLU cc_start: 0.7592 (mp0) cc_final: 0.7336 (mp0)
REVERT: A  233 ASP cc_start: 0.7921 (t0) cc_final: 0.7667 (t70)
REVERT: A  244 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: B   44 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6470 (pp30)
REVERT: B   46 ARG cc_start: 0.7501 (ttm170) cc_final: 0.7207 (ttm170)
REVERT: B   75 GLN cc_start: 0.8179 (tt0) cc_final: 0.7899 (tt0)
REVERT: B  186 ASP cc_start: 0.7800 (m-30) cc_final: 0.7589 (m-30)
REVERT: B  277 SER cc_start: 0.8109 (t) cc_final: 0.7827 (m)
REVERT: C   42 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6932 (mp0)
REVERT: S   76 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8367 (mmmt)
REVERT: S   85 SER cc_start: 0.8289 (t) cc_final: 0.7885 (p)
REVERT: S  109 ASP cc_start: 0.7369 (m-30) cc_final: 0.7136 (m-30)
REVERT: R   34 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7961 (mm)
REVERT: R  140 THR cc_start: 0.8130 (p) cc_final: 0.7914 (m)
REVERT: R  293 LYS cc_start: 0.8157 (mttm) cc_final: 0.7921 (mttm)
REVERT: R  301 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7605 (ttpt)
  outliers start: 38
  outliers final: 11
  residues processed: 231
  average time/residue: 0.5341
  time to fit residues: 132.4085
Evaluate side-chains
  217 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   79 MET
Chi-restraints excluded: chain R residue  180 SER
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0270
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0050
   chunk 57 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   chunk 106 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.2652

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 230 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.148345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131257 restraints weight = 12907.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.82
r_work: 0.3719 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9372  Z= 0.112
  Angle     :  0.536   8.279  12700  Z= 0.276
  Chirality :  0.043   0.191   1455
  Planarity :  0.004   0.059   1602
  Dihedral  :  4.085  26.657   1274
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.63 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.25), residues: 1151
  helix:  2.48 (0.25), residues: 403
  sheet: -0.37 (0.31), residues: 281
  loop : -0.44 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 237 
 TYR   0.016   0.001   TYR R 276 
 PHE   0.023   0.001   PHE A  74 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9367)
  covalent geometry    : angle       0.53545 (12692)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.74236 (    8)
  hydrogen bonds       : bond        0.03857 (  484)
  hydrogen bonds       : angle       4.60306 ( 1377)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7152 (ttmt)
REVERT: A   98 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7192 (pm20)
REVERT: A  148 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7456 (mmt)
REVERT: A  166 GLU cc_start: 0.7608 (mp0) cc_final: 0.7361 (mp0)
REVERT: A  233 ASP cc_start: 0.7895 (t0) cc_final: 0.7629 (t0)
REVERT: A  244 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7616 (mm-30)
REVERT: B   44 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6647 (pp30)
REVERT: B  117 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8200 (mt)
REVERT: B  277 SER cc_start: 0.8120 (t) cc_final: 0.7847 (m)
REVERT: C   42 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6866 (mp0)
REVERT: S   50 TYR cc_start: 0.8400 (t80) cc_final: 0.8085 (t80)
REVERT: S   76 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8305 (mmmt)
REVERT: S   85 SER cc_start: 0.8280 (t) cc_final: 0.7876 (p)
REVERT: S  161 TYR cc_start: 0.8624 (m-80) cc_final: 0.8218 (m-80)
REVERT: S  192 SER cc_start: 0.8547 (m) cc_final: 0.8276 (t)
REVERT: S  223 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.6141 (t80)
REVERT: R   34 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7988 (mm)
REVERT: R   71 TYR cc_start: 0.8220 (t80) cc_final: 0.7970 (t80)
REVERT: R   83 ILE cc_start: 0.7858 (mm) cc_final: 0.7604 (tp)
REVERT: R  121 TYR cc_start: 0.7752 (t80) cc_final: 0.7512 (t80)
REVERT: R  293 LYS cc_start: 0.8152 (mttm) cc_final: 0.7899 (mttm)
REVERT: R  301 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7564 (ttpt)
  outliers start: 37
  outliers final: 12
  residues processed: 230
  average time/residue: 0.4371
  time to fit residues: 108.7494
Evaluate side-chains
  220 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 94 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
R  54 HIS
R  82 ASN
** R 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.147154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.129305 restraints weight = 12571.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.85
r_work: 0.3677 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9372  Z= 0.167
  Angle     :  0.566   7.767  12700  Z= 0.293
  Chirality :  0.044   0.206   1455
  Planarity :  0.005   0.057   1602
  Dihedral  :  4.204  28.489   1274
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 24.83 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1151
  helix:  2.38 (0.25), residues: 403
  sheet: -0.35 (0.32), residues: 268
  loop : -0.51 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 237 
 TYR   0.015   0.002   TYR S 223 
 PHE   0.021   0.002   PHE A  74 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9367)
  covalent geometry    : angle       0.56599 (12692)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       0.84829 (    8)
  hydrogen bonds       : bond        0.04191 (  484)
  hydrogen bonds       : angle       4.71755 ( 1377)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7279 (ttmt)
REVERT: A   98 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7269 (pm20)
REVERT: A  148 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7499 (mmt)
REVERT: A  233 ASP cc_start: 0.7923 (t0) cc_final: 0.7690 (t70)
REVERT: A  244 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: B   44 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6473 (pp30)
REVERT: B   46 ARG cc_start: 0.7445 (ttm170) cc_final: 0.7152 (ttm170)
REVERT: B  117 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (mt)
REVERT: B  277 SER cc_start: 0.8114 (t) cc_final: 0.7805 (m)
REVERT: C   42 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6958 (mp0)
REVERT: S   76 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8333 (mmmt)
REVERT: S   85 SER cc_start: 0.8294 (t) cc_final: 0.7892 (p)
REVERT: S  109 ASP cc_start: 0.7407 (m-30) cc_final: 0.7153 (m-30)
REVERT: S  223 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6125 (t80)
REVERT: R   11 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6975 (tp)
REVERT: R   34 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8005 (mm)
REVERT: R   78 LYS cc_start: 0.8016 (tppt) cc_final: 0.7791 (tppt)
REVERT: R  293 LYS cc_start: 0.8141 (mttm) cc_final: 0.7896 (mttm)
REVERT: R  301 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7584 (ttpt)
  outliers start: 35
  outliers final: 13
  residues processed: 222
  average time/residue: 0.4041
  time to fit residues: 97.1553
Evaluate side-chains
  221 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN
C  59 ASN
S  82 GLN
R  54 HIS
** R 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.147154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129359 restraints weight = 12557.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.85
r_work: 0.3684 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9372  Z= 0.143
  Angle     :  0.558   7.448  12700  Z= 0.287
  Chirality :  0.044   0.203   1455
  Planarity :  0.004   0.058   1602
  Dihedral  :  4.220  33.743   1274
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.62 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1151
  helix:  2.39 (0.25), residues: 403
  sheet: -0.29 (0.32), residues: 271
  loop : -0.55 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 237 
 TYR   0.015   0.002   TYR S 223 
 PHE   0.023   0.002   PHE A  74 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9367)
  covalent geometry    : angle       0.55767 (12692)
  SS BOND              : bond        0.00217 (    4)
  SS BOND              : angle       0.88479 (    8)
  hydrogen bonds       : bond        0.04063 (  484)
  hydrogen bonds       : angle       4.68508 ( 1377)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 200
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7255 (ttmt)
REVERT: A   98 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7220 (pm20)
REVERT: A  148 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7438 (mmt)
REVERT: A  233 ASP cc_start: 0.7938 (t0) cc_final: 0.7705 (t70)
REVERT: A  244 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: B   44 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6701 (pp30)
REVERT: B  117 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: B  277 SER cc_start: 0.8116 (t) cc_final: 0.7797 (m)
REVERT: C   42 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6910 (mp0)
REVERT: S   76 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8306 (mmmt)
REVERT: S   85 SER cc_start: 0.8292 (t) cc_final: 0.7888 (p)
REVERT: S  223 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.6132 (t80)
REVERT: R   11 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6943 (tp)
REVERT: R   34 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7983 (mm)
REVERT: R   71 TYR cc_start: 0.8227 (t80) cc_final: 0.8010 (t80)
REVERT: R   78 LYS cc_start: 0.7958 (tppt) cc_final: 0.7697 (tppt)
REVERT: R  293 LYS cc_start: 0.8105 (mttm) cc_final: 0.7853 (mttm)
REVERT: R  301 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7598 (ttpt)
  outliers start: 35
  outliers final: 18
  residues processed: 218
  average time/residue: 0.4212
  time to fit residues: 99.5043
Evaluate side-chains
  225 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  194 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    0.0470
   chunk 43 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0370
   chunk 103 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.147339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129449 restraints weight = 12503.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.85
r_work: 0.3684 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9372  Z= 0.143
  Angle     :  0.561   7.490  12700  Z= 0.290
  Chirality :  0.044   0.198   1455
  Planarity :  0.004   0.059   1602
  Dihedral  :  4.204  32.696   1274
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.21 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.25), residues: 1151
  helix:  2.38 (0.25), residues: 403
  sheet: -0.17 (0.32), residues: 274
  loop : -0.55 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 237 
 TYR   0.015   0.002   TYR R 276 
 PHE   0.023   0.002   PHE A  74 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9367)
  covalent geometry    : angle       0.56043 (12692)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       0.82647 (    8)
  hydrogen bonds       : bond        0.04057 (  484)
  hydrogen bonds       : angle       4.68654 ( 1377)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7228 (ttmt)
REVERT: A   98 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7161 (pm20)
REVERT: A  117 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7526 (mtm-85)
REVERT: A  148 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7436 (mmt)
REVERT: A  233 ASP cc_start: 0.7915 (t0) cc_final: 0.7675 (t70)
REVERT: A  244 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: B   44 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6729 (pp30)
REVERT: B  277 SER cc_start: 0.8105 (t) cc_final: 0.7785 (m)
REVERT: C   42 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: S   76 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8293 (mmmt)
REVERT: S   85 SER cc_start: 0.8287 (t) cc_final: 0.7880 (p)
REVERT: S  161 TYR cc_start: 0.8675 (m-80) cc_final: 0.8304 (m-80)
REVERT: S  223 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.6093 (t80)
REVERT: R   11 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6957 (tp)
REVERT: R   34 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7979 (mm)
REVERT: R   71 TYR cc_start: 0.8251 (t80) cc_final: 0.7936 (t80)
REVERT: R   78 LYS cc_start: 0.7943 (tppt) cc_final: 0.7713 (tppt)
REVERT: R  293 LYS cc_start: 0.8096 (mttm) cc_final: 0.7841 (mttm)
REVERT: R  301 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7600 (ttpt)
  outliers start: 31
  outliers final: 15
  residues processed: 219
  average time/residue: 0.4975
  time to fit residues: 117.2779
Evaluate side-chains
  220 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  194 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   chunk 104 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0980
   chunk 105 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 230 ASN
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.147665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.129820 restraints weight = 12561.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.85
r_work: 0.3688 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9372  Z= 0.138
  Angle     :  0.565   7.048  12700  Z= 0.291
  Chirality :  0.044   0.204   1455
  Planarity :  0.004   0.058   1602
  Dihedral  :  4.204  32.143   1274
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.51 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.25), residues: 1151
  helix:  2.28 (0.25), residues: 408
  sheet: -0.20 (0.32), residues: 282
  loop : -0.43 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 232 
 TYR   0.015   0.002   TYR S  59 
 PHE   0.024   0.002   PHE A  74 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9367)
  covalent geometry    : angle       0.56517 (12692)
  SS BOND              : bond        0.00228 (    4)
  SS BOND              : angle       0.57367 (    8)
  hydrogen bonds       : bond        0.04022 (  484)
  hydrogen bonds       : angle       4.67312 ( 1377)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7220 (ttmt)
REVERT: A   98 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7156 (pm20)
REVERT: A  117 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7501 (mtm-85)
REVERT: A  148 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7454 (mmt)
REVERT: A  233 ASP cc_start: 0.7935 (t0) cc_final: 0.7696 (t70)
REVERT: A  244 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7663 (mm-30)
REVERT: B   44 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6782 (pp30)
REVERT: B  152 LEU cc_start: 0.8158 (mt) cc_final: 0.7931 (mm)
REVERT: B  277 SER cc_start: 0.8102 (t) cc_final: 0.7784 (m)
REVERT: C   42 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6937 (mp0)
REVERT: S   76 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8269 (mmmt)
REVERT: S   85 SER cc_start: 0.8288 (t) cc_final: 0.7883 (p)
REVERT: S  161 TYR cc_start: 0.8649 (m-80) cc_final: 0.8196 (m-80)
REVERT: S  223 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.6094 (t80)
REVERT: R   11 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6965 (tp)
REVERT: R   34 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7972 (mm)
REVERT: R   71 TYR cc_start: 0.8265 (t80) cc_final: 0.7856 (t80)
REVERT: R   78 LYS cc_start: 0.7905 (tppt) cc_final: 0.7702 (tppt)
REVERT: R  121 TYR cc_start: 0.7760 (t80) cc_final: 0.7488 (t80)
REVERT: R  293 LYS cc_start: 0.8114 (mttm) cc_final: 0.7858 (mttm)
REVERT: R  301 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7604 (ttpt)
  outliers start: 33
  outliers final: 17
  residues processed: 220
  average time/residue: 0.4936
  time to fit residues: 116.8295
Evaluate side-chains
  223 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  194 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Chi-restraints excluded: chain R residue  258 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 230 ASN
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4003 r_free = 0.4003 target = 0.146546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.129366 restraints weight = 12823.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.82
r_work: 0.3686 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9372  Z= 0.149
  Angle     :  0.583   8.876  12700  Z= 0.296
  Chirality :  0.044   0.222   1455
  Planarity :  0.004   0.059   1602
  Dihedral  :  4.203  31.266   1274
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.90 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.25), residues: 1151
  helix:  2.38 (0.25), residues: 403
  sheet: -0.15 (0.32), residues: 275
  loop : -0.47 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 232 
 TYR   0.018   0.002   TYR S  59 
 PHE   0.023   0.002   PHE A  74 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9367)
  covalent geometry    : angle       0.58313 (12692)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       0.30929 (    8)
  hydrogen bonds       : bond        0.04079 (  484)
  hydrogen bonds       : angle       4.69179 ( 1377)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7229 (ttmt)
REVERT: A   98 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7155 (pm20)
REVERT: A  117 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7498 (mtm-85)
REVERT: A  148 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7419 (mmt)
REVERT: A  233 ASP cc_start: 0.7910 (t0) cc_final: 0.7666 (t70)
REVERT: A  244 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: B   44 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6805 (pp30)
REVERT: B  152 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7977 (mm)
REVERT: B  277 SER cc_start: 0.8102 (t) cc_final: 0.7773 (m)
REVERT: C   42 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6946 (mp0)
REVERT: S   85 SER cc_start: 0.8286 (t) cc_final: 0.7877 (p)
REVERT: S  118 THR cc_start: 0.8179 (m) cc_final: 0.7930 (p)
REVERT: S  161 TYR cc_start: 0.8644 (m-80) cc_final: 0.8251 (m-80)
REVERT: S  203 THR cc_start: 0.7314 (m) cc_final: 0.7029 (p)
REVERT: S  223 TYR cc_start: 0.6411 (OUTLIER) cc_final: 0.6067 (t80)
REVERT: R   11 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6953 (tp)
REVERT: R   34 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (mm)
REVERT: R   71 TYR cc_start: 0.8264 (t80) cc_final: 0.7789 (t80)
REVERT: R  200 LEU cc_start: 0.8020 (tp) cc_final: 0.7768 (tt)
REVERT: R  293 LYS cc_start: 0.8118 (mttm) cc_final: 0.7868 (mttm)
REVERT: R  301 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7613 (ttpt)
  outliers start: 31
  outliers final: 19
  residues processed: 222
  average time/residue: 0.4765
  time to fit residues: 114.2139
Evaluate side-chains
  232 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 204
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  194 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   11 ILE
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue  220 ILE
Chi-restraints excluded: chain R residue  237 SER
Chi-restraints excluded: chain R residue  256 MET
Chi-restraints excluded: chain R residue  258 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 230 ASN
S  82 GLN
R  54 HIS
** R 163 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.146192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.128154 restraints weight = 12390.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.84
r_work: 0.3668 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9372  Z= 0.181
  Angle     :  0.606   8.792  12700  Z= 0.309
  Chirality :  0.045   0.229   1455
  Planarity :  0.005   0.058   1602
  Dihedral  :  4.300  29.522   1274
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.00 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.25), residues: 1151
  helix:  2.31 (0.25), residues: 403
  sheet: -0.21 (0.32), residues: 276
  loop : -0.47 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 232 
 TYR   0.021   0.002   TYR S  59 
 PHE   0.022   0.002   PHE A  74 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9367)
  covalent geometry    : angle       0.60567 (12692)
  SS BOND              : bond        0.00206 (    4)
  SS BOND              : angle       0.28480 (    8)
  hydrogen bonds       : bond        0.04265 (  484)
  hydrogen bonds       : angle       4.77049 ( 1377)
  Misc. bond           : bond        0.00003 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3962.54 seconds
wall clock time: 68 minutes 11.76 seconds (4091.76 seconds total)