Starting phenix.real_space_refine
on Sat Oct 11 18:15:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683_neut_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irr_35683/10_2025/8irr_35683.map"
  }
  resolution = 3.2
  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=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 438 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5259      2.51       5
     N    1424      2.21       5
     O    1511      1.98       5
     H    8080      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16329
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 3744
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5108
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 882
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1913
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 4570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 4570
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 10, 'TRANS': 271}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 112
          Unusual residues: {'CLR': 3, 'R5F': 1}
          Classifications: {'undetermined': 4, 'water': 2}
          Link IDs: {None: 5}
  Time building chain proxies: 2.84, per 1000 atoms: 0.17
  Number of scatterers: 16329
  At special positions: 0
  Unit cell: (100, 106.4, 116, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     O    1511      8.00
     N    1424      7.00
     C    5259      6.00
     H    8080      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 458.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      45.3% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 120 through 134
    Processing helix  chain 'A' and resid 148 through 158
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 172
    Processing helix  chain 'A' and resid 186 through 206
      removed outlier: 3.761A  pdb=" N   PHE A 200 " --> pdb=" O   ILE A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 246
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.501A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.547A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.744A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.563A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'N' and resid 107 through 112
      removed outlier: 3.689A  pdb=" N   VAL N 110 " --> pdb=" O   CYS N 107 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   THR N 111 " --> pdb=" O   PHE N 108 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 51
    Processing helix  chain 'R' and resid 51 through 57
      removed outlier: 3.762A  pdb=" N   ARG R  55 " --> pdb=" O   PHE R  51 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS R  57 " --> pdb=" O   HIS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 77
      removed outlier: 3.829A  pdb=" N   PHE R  61 " --> pdb=" O   LYS R  57 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
      removed outlier: 3.553A  pdb=" N   LYS R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 95 through 127
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 161
      removed outlier: 3.599A  pdb=" N   SER R 155 " --> pdb=" O   SER R 151 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 240
    Processing helix  chain 'R' and resid 264 through 298
      removed outlier: 3.532A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 3.721A  pdb=" N   CYS R 293 " --> pdb=" O   PHE R 289 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 309 through 332
      removed outlier: 3.931A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 345
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76
      removed outlier: 9.121A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   HIS A 217 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.697A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.366A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.767A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.639A  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 151
      removed outlier: 3.606A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.552A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.165A  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: 6.650A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.679A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.724A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    446 hydrogen bonds defined for protein.
    1260 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: 3.56

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 8045
        1.13 -     1.30: 1452
        1.30 -     1.47: 3227
        1.47 -     1.65: 3705
        1.65 -     1.82: 75
  Bond restraints: 16504
  Sorted by residual:
  bond pdb=" NH1 ARG A 191 "
       pdb="HH12 ARG A 191 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CD2 PHE R 129 "
       pdb=" HD2 PHE R 129 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   SER N  63 "
       pdb=" H   SER N  63 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   PHE N  29 "
       pdb=" H   PHE N  29 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   GLY B 216 "
       pdb=" H   GLY B 216 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 16499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 24460
        2.15 -     4.30: 3598
        4.30 -     6.45: 1179
        6.45 -     8.59: 396
        8.59 -    10.74: 7
  Bond angle restraints: 29640
  Sorted by residual:
  angle pdb=" N   ILE B  58 "
        pdb=" CA  ILE B  58 "
        pdb=" C   ILE B  58 "
      ideal   model   delta    sigma   weight residual
     109.58  100.79    8.79 1.29e+00 6.01e-01 4.64e+01
  angle pdb=" CA  ASN B 119 "
        pdb=" CB  ASN B 119 "
        pdb=" CG  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     112.60  118.64   -6.04 1.00e+00 1.00e+00 3.64e+01
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     109.24  119.98  -10.74 1.89e+00 2.80e-01 3.23e+01
  angle pdb=" C   CYS B 204 "
        pdb=" N   ASP B 205 "
        pdb=" CA  ASP B 205 "
      ideal   model   delta    sigma   weight residual
     121.87  131.16   -9.29 1.64e+00 3.72e-01 3.21e+01
  angle pdb=" N   ALA B  60 "
        pdb=" CA  ALA B  60 "
        pdb=" C   ALA B  60 "
      ideal   model   delta    sigma   weight residual
     108.42  116.77   -8.35 1.54e+00 4.22e-01 2.94e+01
  ... (remaining 29635 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 7176
       17.41 -    34.82: 473
       34.82 -    52.23: 132
       52.23 -    69.64: 156
       69.64 -    87.05: 10
  Dihedral angle restraints: 7947
    sinusoidal: 4357
      harmonic: 3590
  Sorted by residual:
  dihedral pdb=" C   ASN B 119 "
           pdb=" N   ASN B 119 "
           pdb=" CA  ASN B 119 "
           pdb=" CB  ASN B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.21   15.61     0      2.50e+00 1.60e-01 3.90e+01
  dihedral pdb=" CA  MET B  61 "
           pdb=" C   MET B  61 "
           pdb=" N   HIS B  62 "
           pdb=" CA  HIS B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.52   29.48     0      5.00e+00 4.00e-02 3.48e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.79   29.21     0      5.00e+00 4.00e-02 3.41e+01
  ... (remaining 7944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1049
       0.116 -    0.232: 221
       0.232 -    0.348: 21
       0.348 -    0.464: 4
       0.464 -    0.580: 1
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" CA  ASN B 119 "
            pdb=" N   ASN B 119 "
            pdb=" C   ASN B 119 "
            pdb=" CB  ASN B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.40e+00
  chirality pdb=" CA  GLN B  75 "
            pdb=" N   GLN B  75 "
            pdb=" C   GLN B  75 "
            pdb=" CB  GLN B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.07e+00
  chirality pdb=" CA  ALA B 302 "
            pdb=" N   ALA B 302 "
            pdb=" C   ALA B 302 "
            pdb=" CB  ALA B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.10    0.38 2.00e-01 2.50e+01 3.62e+00
  ... (remaining 1293 not shown)

  Planarity restraints: 2425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 148 "    0.230 2.00e-02 2.50e+03   9.78e-02 3.82e+02
        pdb=" CG  TRP R 148 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 148 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 148 "   -0.058 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 148 "   -0.070 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 148 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 148 "   -0.086 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 148 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 148 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 148 "    0.066 2.00e-02 2.50e+03
        pdb=" HD1 TRP R 148 "    0.025 2.00e-02 2.50e+03
        pdb=" HE1 TRP R 148 "   -0.136 2.00e-02 2.50e+03
        pdb=" HE3 TRP R 148 "   -0.154 2.00e-02 2.50e+03
        pdb=" HZ2 TRP R 148 "    0.046 2.00e-02 2.50e+03
        pdb=" HZ3 TRP R 148 "   -0.045 2.00e-02 2.50e+03
        pdb=" HH2 TRP R 148 "    0.166 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "    0.185 2.00e-02 2.50e+03   6.92e-02 1.92e+02
        pdb=" CG  TRP B  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "   -0.083 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "    0.039 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  63 "    0.027 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  63 "   -0.055 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  63 "   -0.102 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  63 "    0.044 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  63 "    0.012 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  63 "    0.091 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 285 "    0.072 2.00e-02 2.50e+03   6.26e-02 1.57e+02
        pdb=" CG  TRP R 285 "    0.079 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 285 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 285 "    0.053 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 285 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 285 "    0.032 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 285 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 285 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 285 "   -0.050 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 285 "    0.020 2.00e-02 2.50e+03
        pdb=" HD1 TRP R 285 "   -0.088 2.00e-02 2.50e+03
        pdb=" HE1 TRP R 285 "   -0.078 2.00e-02 2.50e+03
        pdb=" HE3 TRP R 285 "    0.003 2.00e-02 2.50e+03
        pdb=" HZ2 TRP R 285 "    0.055 2.00e-02 2.50e+03
        pdb=" HZ3 TRP R 285 "   -0.145 2.00e-02 2.50e+03
        pdb=" HH2 TRP R 285 "    0.060 2.00e-02 2.50e+03
  ... (remaining 2422 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 480
        2.03 -     2.67: 21014
        2.67 -     3.32: 49625
        3.32 -     3.96: 65577
        3.96 -     4.60: 96032
  Nonbonded interactions: 232728
  Sorted by model distance:
  nonbonded pdb=" HA  VAL B 315 "
            pdb=" HG  SER B 331 "
     model   vdw
     1.388 2.270
  nonbonded pdb=" HG  SER N  52 "
            pdb=" H   GLN N  53 "
     model   vdw
     1.401 2.100
  nonbonded pdb="HD21 ASN A  50 "
            pdb=" HD3 ARG A 120 "
     model   vdw
     1.462 2.270
  nonbonded pdb=" HE2 HIS B  54 "
            pdb=" HG  SER B  72 "
     model   vdw
     1.507 2.100
  nonbonded pdb=" OE2 GLU B 226 "
            pdb=" HH  TYR N  32 "
     model   vdw
     1.626 2.450
  ... (remaining 232723 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.480
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
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      :  0.012   0.070   8427  Z= 0.747
  Angle     :  1.804  10.742  11432  Z= 1.213
  Chirality :  0.095   0.580   1296
  Planarity :  0.016   0.124   1433
  Dihedral  : 12.313  87.049   3211
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.24), residues: 1012
  helix:  0.07 (0.22), residues: 410
  sheet:  0.71 (0.37), residues: 189
  loop : -0.94 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 191 
 TYR   0.076   0.015   TYR R 194 
 PHE   0.120   0.015   PHE N  68 
 TRP   0.135   0.029   TRP R 148 
 HIS   0.025   0.006   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.01229 ( 8424)
  covalent geometry    : angle       1.80322 (11426)
  SS BOND              : bond        0.00803 (    3)
  SS BOND              : angle       2.68762 (    6)
  hydrogen bonds       : bond        0.14680 (  446)
  hydrogen bonds       : angle       7.24966 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7064 (mm-30)
REVERT: A   29 GLN cc_start: 0.8237 (tp40) cc_final: 0.7980 (tp40)
REVERT: A   32 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7604 (mttt)
REVERT: A   33 ASP cc_start: 0.7179 (m-30) cc_final: 0.6917 (m-30)
REVERT: A  186 ASP cc_start: 0.6814 (t70) cc_final: 0.6446 (m-30)
REVERT: B   44 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6893 (mm-40)
REVERT: G   14 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8175 (mmtm)
REVERT: R  223 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8060 (mmtm)
REVERT: R  339 LYS cc_start: 0.8099 (tttm) cc_final: 0.7830 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2664
  time to fit residues: 82.1380
Evaluate side-chains
  171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
B  32 GLN
B  75 GLN
G  18 GLN
N  82 GLN
N  84 ASN
R 164 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.120057 restraints weight = 27156.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.14
r_work: 0.3257 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8427  Z= 0.152
  Angle     :  0.630   7.080  11432  Z= 0.346
  Chirality :  0.042   0.146   1296
  Planarity :  0.005   0.040   1433
  Dihedral  :  6.081  42.920   1337
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  5.75 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1012
  helix:  1.40 (0.24), residues: 416
  sheet: -0.10 (0.35), residues: 201
  loop : -0.80 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  67 
 TYR   0.013   0.002   TYR A 194 
 PHE   0.025   0.002   PHE R 288 
 TRP   0.018   0.002   TRP R  80 
 HIS   0.005   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8424)
  covalent geometry    : angle       0.62995 (11426)
  SS BOND              : bond        0.00520 (    3)
  SS BOND              : angle       0.71972 (    6)
  hydrogen bonds       : bond        0.05261 (  446)
  hydrogen bonds       : angle       5.45454 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8239 (tp40) cc_final: 0.7826 (tp-100)
REVERT: A   33 ASP cc_start: 0.7438 (m-30) cc_final: 0.7139 (m-30)
REVERT: A  186 ASP cc_start: 0.7432 (t70) cc_final: 0.6761 (m-30)
REVERT: A  198 ASP cc_start: 0.8480 (m-30) cc_final: 0.8239 (m-30)
REVERT: G   14 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7930 (mtmm)
REVERT: G   38 MET cc_start: 0.8184 (ttp) cc_final: 0.7933 (ttp)
  outliers start: 11
  outliers final: 8
  residues processed: 181
  average time/residue: 0.2336
  time to fit residues: 54.3716
Evaluate side-chains
  160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain N residue   82 GLN
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B  75 GLN
B  88 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.115977 restraints weight = 27669.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.15
r_work: 0.3212 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   8427  Z= 0.187
  Angle     :  0.568   6.325  11432  Z= 0.314
  Chirality :  0.041   0.138   1296
  Planarity :  0.004   0.041   1433
  Dihedral  :  5.729  39.658   1337
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.13 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.26), residues: 1012
  helix:  1.58 (0.24), residues: 419
  sheet: -0.33 (0.35), residues: 205
  loop : -0.78 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.013   0.001   TYR A 194 
 PHE   0.016   0.002   PHE N  68 
 TRP   0.014   0.002   TRP A  96 
 HIS   0.006   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8424)
  covalent geometry    : angle       0.56748 (11426)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       1.19307 (    6)
  hydrogen bonds       : bond        0.04719 (  446)
  hydrogen bonds       : angle       5.12653 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8198 (tp40) cc_final: 0.7801 (tp-100)
REVERT: A   33 ASP cc_start: 0.7541 (m-30) cc_final: 0.7213 (m-30)
REVERT: A  186 ASP cc_start: 0.7327 (t70) cc_final: 0.6618 (m-30)
REVERT: A  198 ASP cc_start: 0.8618 (m-30) cc_final: 0.8243 (m-30)
REVERT: B  263 THR cc_start: 0.8970 (t) cc_final: 0.8753 (m)
REVERT: G   14 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7915 (mtmm)
REVERT: G   38 MET cc_start: 0.8234 (ttp) cc_final: 0.8005 (ttp)
  outliers start: 10
  outliers final: 8
  residues processed: 176
  average time/residue: 0.2432
  time to fit residues: 55.5748
Evaluate side-chains
  163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  333 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118029 restraints weight = 27287.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.15
r_work: 0.3240 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8427  Z= 0.123
  Angle     :  0.510   5.670  11432  Z= 0.277
  Chirality :  0.039   0.136   1296
  Planarity :  0.004   0.038   1433
  Dihedral  :  5.308  31.704   1337
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.03 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.26), residues: 1012
  helix:  1.96 (0.25), residues: 413
  sheet: -0.47 (0.35), residues: 205
  loop : -0.60 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.011   0.001   TYR A 194 
 PHE   0.014   0.001   PHE R 288 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.004   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8424)
  covalent geometry    : angle       0.50991 (11426)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       0.69466 (    6)
  hydrogen bonds       : bond        0.04237 (  446)
  hydrogen bonds       : angle       4.83956 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8114 (tp40) cc_final: 0.7691 (tp-100)
REVERT: A   33 ASP cc_start: 0.7504 (m-30) cc_final: 0.7149 (m-30)
REVERT: A  186 ASP cc_start: 0.7226 (t70) cc_final: 0.6516 (m-30)
REVERT: A  198 ASP cc_start: 0.8595 (m-30) cc_final: 0.8230 (m-30)
REVERT: G   14 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7890 (mtmm)
REVERT: G   21 MET cc_start: 0.8107 (ttp) cc_final: 0.7730 (tpt)
REVERT: N   32 TYR cc_start: 0.8700 (m-80) cc_final: 0.8040 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 175
  average time/residue: 0.2342
  time to fit residues: 53.3194
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.0270
   chunk 53 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 99 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    1.7844

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  82 GLN
R 323 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.116769 restraints weight = 27308.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.14
r_work: 0.3223 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8427  Z= 0.149
  Angle     :  0.504   5.561  11432  Z= 0.276
  Chirality :  0.039   0.136   1296
  Planarity :  0.004   0.040   1433
  Dihedral  :  5.266  33.381   1337
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.60 %
    Favored  : 87.71 %
  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 aren not related in a simple way.
  whole:  0.63 (0.26), residues: 1012
  helix:  2.06 (0.25), residues: 414
  sheet: -0.73 (0.34), residues: 217
  loop : -0.65 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.004   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8424)
  covalent geometry    : angle       0.50393 (11426)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       0.79023 (    6)
  hydrogen bonds       : bond        0.04120 (  446)
  hydrogen bonds       : angle       4.74548 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8110 (tp40) cc_final: 0.7632 (tp-100)
REVERT: A   32 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7659 (mtmm)
REVERT: A   33 ASP cc_start: 0.7596 (m-30) cc_final: 0.7225 (m-30)
REVERT: A  186 ASP cc_start: 0.7198 (t70) cc_final: 0.6470 (m-30)
REVERT: A  198 ASP cc_start: 0.8693 (m-30) cc_final: 0.8396 (m-30)
REVERT: G   14 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7887 (mtmm)
REVERT: G   21 MET cc_start: 0.8096 (ttp) cc_final: 0.7710 (tpt)
REVERT: N   13 GLN cc_start: 0.7642 (mp10) cc_final: 0.7410 (mm-40)
REVERT: R  339 LYS cc_start: 0.8177 (tttm) cc_final: 0.7817 (tttp)
  outliers start: 15
  outliers final: 13
  residues processed: 165
  average time/residue: 0.2545
  time to fit residues: 53.6854
Evaluate side-chains
  159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  323 ASN
Chi-restraints excluded: chain R residue  333 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.148703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115963 restraints weight = 27564.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.15
r_work: 0.3216 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8427  Z= 0.155
  Angle     :  0.502   5.637  11432  Z= 0.275
  Chirality :  0.039   0.134   1296
  Planarity :  0.004   0.051   1433
  Dihedral  :  5.265  34.961   1337
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.60 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.27), residues: 1012
  helix:  2.10 (0.25), residues: 414
  sheet: -0.85 (0.34), residues: 217
  loop : -0.61 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 172 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.013   0.001   PHE R 288 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8424)
  covalent geometry    : angle       0.50204 (11426)
  SS BOND              : bond        0.00264 (    3)
  SS BOND              : angle       0.72747 (    6)
  hydrogen bonds       : bond        0.04103 (  446)
  hydrogen bonds       : angle       4.71940 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8060 (tp40) cc_final: 0.7642 (tp-100)
REVERT: A   32 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7633 (mtmm)
REVERT: A   33 ASP cc_start: 0.7562 (m-30) cc_final: 0.7186 (m-30)
REVERT: A  186 ASP cc_start: 0.7191 (t70) cc_final: 0.6470 (m-30)
REVERT: A  198 ASP cc_start: 0.8695 (m-30) cc_final: 0.8405 (m-30)
REVERT: G   14 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7899 (mtmm)
REVERT: G   21 MET cc_start: 0.8129 (ttp) cc_final: 0.7719 (tpt)
REVERT: N   13 GLN cc_start: 0.7652 (mp10) cc_final: 0.7398 (mm-40)
REVERT: N   89 GLU cc_start: 0.7674 (tt0) cc_final: 0.7471 (pt0)
REVERT: R  339 LYS cc_start: 0.8182 (tttm) cc_final: 0.7802 (tttp)
  outliers start: 18
  outliers final: 15
  residues processed: 159
  average time/residue: 0.2268
  time to fit residues: 47.1083
Evaluate side-chains
  159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  126 SER
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  268 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.145316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.111704 restraints weight = 27771.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.22
r_work: 0.3159 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   8427  Z= 0.252
  Angle     :  0.574   6.341  11432  Z= 0.316
  Chirality :  0.042   0.146   1296
  Planarity :  0.005   0.044   1433
  Dihedral  :  5.828  44.619   1337
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.05 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1012
  helix:  1.77 (0.25), residues: 413
  sheet: -1.11 (0.33), residues: 219
  loop : -0.66 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 172 
 TYR   0.015   0.002   TYR A 194 
 PHE   0.016   0.002   PHE A  74 
 TRP   0.011   0.002   TRP A  96 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 8424)
  covalent geometry    : angle       0.57337 (11426)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       0.94208 (    6)
  hydrogen bonds       : bond        0.04412 (  446)
  hydrogen bonds       : angle       4.94410 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7572 (mtmm)
REVERT: A   33 ASP cc_start: 0.7683 (m-30) cc_final: 0.7287 (m-30)
REVERT: A  186 ASP cc_start: 0.7208 (t70) cc_final: 0.6483 (m-30)
REVERT: G   14 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7823 (mtmm)
REVERT: G   21 MET cc_start: 0.8194 (ttp) cc_final: 0.7737 (tpt)
REVERT: N   13 GLN cc_start: 0.7624 (mp10) cc_final: 0.7331 (mm-40)
REVERT: N   89 GLU cc_start: 0.7865 (tt0) cc_final: 0.7631 (pt0)
REVERT: R  339 LYS cc_start: 0.8178 (tttm) cc_final: 0.7910 (tttp)
  outliers start: 23
  outliers final: 20
  residues processed: 164
  average time/residue: 0.2444
  time to fit residues: 51.5955
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  126 SER
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  268 THR
Chi-restraints excluded: chain R residue  333 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.0970
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 75 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.3382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.148525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115741 restraints weight = 27583.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.15
r_work: 0.3216 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8427  Z= 0.123
  Angle     :  0.494   5.597  11432  Z= 0.269
  Chirality :  0.039   0.135   1296
  Planarity :  0.004   0.067   1433
  Dihedral  :  5.325  47.008   1337
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.95 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.27), residues: 1012
  helix:  2.08 (0.25), residues: 413
  sheet: -1.03 (0.34), residues: 217
  loop : -0.59 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.010   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 297 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8424)
  covalent geometry    : angle       0.49401 (11426)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.69295 (    6)
  hydrogen bonds       : bond        0.03980 (  446)
  hydrogen bonds       : angle       4.70819 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7584 (mtmm)
REVERT: A   33 ASP cc_start: 0.7630 (m-30) cc_final: 0.7241 (m-30)
REVERT: A  186 ASP cc_start: 0.7155 (t70) cc_final: 0.6435 (m-30)
REVERT: A  198 ASP cc_start: 0.8653 (m-30) cc_final: 0.8332 (m-30)
REVERT: G   14 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8004 (mmmt)
REVERT: G   21 MET cc_start: 0.8119 (ttp) cc_final: 0.7708 (tpt)
REVERT: N   13 GLN cc_start: 0.7684 (mp10) cc_final: 0.7374 (mm-40)
REVERT: R  339 LYS cc_start: 0.8206 (tttm) cc_final: 0.7806 (tttp)
  outliers start: 15
  outliers final: 13
  residues processed: 160
  average time/residue: 0.2446
  time to fit residues: 51.1274
Evaluate side-chains
  161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  126 SER
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.147212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114452 restraints weight = 27537.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.14
r_work: 0.3199 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8427  Z= 0.165
  Angle     :  0.509   5.727  11432  Z= 0.278
  Chirality :  0.040   0.147   1296
  Planarity :  0.004   0.046   1433
  Dihedral  :  5.438  50.810   1337
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.61 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.27), residues: 1012
  helix:  2.09 (0.25), residues: 413
  sheet: -1.08 (0.34), residues: 217
  loop : -0.58 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.012   0.001   TYR A 194 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.003   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8424)
  covalent geometry    : angle       0.50917 (11426)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.86151 (    6)
  hydrogen bonds       : bond        0.04052 (  446)
  hydrogen bonds       : angle       4.73290 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7581 (mtmm)
REVERT: A   33 ASP cc_start: 0.7658 (m-30) cc_final: 0.7268 (m-30)
REVERT: A  186 ASP cc_start: 0.7147 (t70) cc_final: 0.6459 (m-30)
REVERT: A  198 ASP cc_start: 0.8687 (m-30) cc_final: 0.8053 (m-30)
REVERT: G   14 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8004 (mmmt)
REVERT: G   21 MET cc_start: 0.8160 (ttp) cc_final: 0.7745 (tpt)
REVERT: N   13 GLN cc_start: 0.7658 (mp10) cc_final: 0.7358 (mm-40)
REVERT: R  339 LYS cc_start: 0.8200 (tttm) cc_final: 0.7915 (tttp)
  outliers start: 17
  outliers final: 14
  residues processed: 161
  average time/residue: 0.2463
  time to fit residues: 51.2858
Evaluate side-chains
  163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  126 SER
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 70 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.116155 restraints weight = 27450.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.20
r_work: 0.3216 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8427  Z= 0.124
  Angle     :  0.484   5.380  11432  Z= 0.263
  Chirality :  0.039   0.145   1296
  Planarity :  0.004   0.063   1433
  Dihedral  :  5.264  53.084   1337
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.18 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.27), residues: 1012
  helix:  2.25 (0.25), residues: 413
  sheet: -1.05 (0.34), residues: 217
  loop : -0.56 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  27 
 TYR   0.010   0.001   TYR A 194 
 PHE   0.013   0.001   PHE R 288 
 TRP   0.011   0.001   TRP R  80 
 HIS   0.003   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8424)
  covalent geometry    : angle       0.48372 (11426)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.74210 (    6)
  hydrogen bonds       : bond        0.03886 (  446)
  hydrogen bonds       : angle       4.63424 ( 1260)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7489 (mtmm)
REVERT: A   33 ASP cc_start: 0.7640 (m-30) cc_final: 0.7222 (m-30)
REVERT: A  186 ASP cc_start: 0.7089 (t70) cc_final: 0.6389 (m-30)
REVERT: G   14 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7971 (mmmt)
REVERT: G   21 MET cc_start: 0.8170 (ttp) cc_final: 0.7713 (tpt)
REVERT: N    6 GLU cc_start: 0.6324 (mp0) cc_final: 0.6000 (mp0)
REVERT: N   13 GLN cc_start: 0.7636 (mp10) cc_final: 0.7320 (mm-40)
REVERT: R  339 LYS cc_start: 0.8169 (tttm) cc_final: 0.7888 (tttp)
  outliers start: 12
  outliers final: 12
  residues processed: 159
  average time/residue: 0.2566
  time to fit residues: 52.5562
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  126 SER
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    9.9990
   chunk 6 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.117832 restraints weight = 27339.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.19
r_work: 0.3245 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8427  Z= 0.105
  Angle     :  0.466   5.245  11432  Z= 0.253
  Chirality :  0.039   0.141   1296
  Planarity :  0.004   0.059   1433
  Dihedral  :  5.066  53.426   1337
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.18 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.27), residues: 1012
  helix:  2.46 (0.25), residues: 409
  sheet: -0.92 (0.34), residues: 215
  loop : -0.52 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  27 
 TYR   0.010   0.001   TYR A 194 
 PHE   0.012   0.001   PHE R 297 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8424)
  covalent geometry    : angle       0.46554 (11426)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       0.75802 (    6)
  hydrogen bonds       : bond        0.03733 (  446)
  hydrogen bonds       : angle       4.50580 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4161.41 seconds
wall clock time: 71 minutes 17.59 seconds (4277.59 seconds total)