Starting phenix.real_space_refine
on Thu Jul  2 19:13:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vug_32127/07_2026/7vug_32127.cif"
  }
  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=   0.001 sd=   0.022
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 1050 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      61      5.16       5
     Cl      1      4.86       5
     C    5711      2.51       5
     N    1503      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8924
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1756
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2324
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 282, 2313
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 12, 'TRANS': 269}
      Conformer: "B"
        Number of residues, atoms: 282, 2313
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 12, 'TRANS': 269}
          bond proxies already assigned to first conformer: 2369
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'7ZQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.24
  Number of scatterers: 8924
  At special positions: 0
  Unit cell: (88.4, 121.68, 125.84, 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)
     Cl      1     17.00
     S      61     16.00
     O    1648      8.00
     N    1503      7.00
     C    5711      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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: 0.79
  Conformation dependent library (CDL) restraints added in 393.6 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 16 sheets defined
      38.2% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 44 through 54
      removed outlier: 3.617A  pdb=" N   THR A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.380A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.080A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.578A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 23 through 25
      No H-bonds generated for 'chain 'R' and resid 23 through 25'
    Processing helix  chain 'R' and resid 26 through 52
      removed outlier: 4.209A  pdb=" N   VAL R  30 " --> pdb=" O   GLY R  26 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL R  31 " --> pdb=" O   PHE R  27 " (cutoff:3.500A)
      Proline residue:  R  42  - end of helix
    Processing helix  chain 'R' and resid 53 through 58
    Processing helix  chain 'R' and resid 60 through 81
      removed outlier: 3.697A  pdb=" N   ASN R  64 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 83 through 88
    Processing helix  chain 'R' and resid 99 through 132
      removed outlier: 3.808A  pdb=" N   THR R 119 " --> pdb=" O   SER R 115 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL R 120 " --> pdb=" O   ILE R 116 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 135 through 140
    Processing helix  chain 'R' and resid 141 through 160
      removed outlier: 3.592A  pdb=" N   LYS R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 166
      removed outlier: 3.714A  pdb=" N   TRP R 165 " --> pdb=" O   PRO R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 192
    Processing helix  chain 'R' and resid 192 through 212
    Processing helix  chain 'R' and resid 220 through 242
      removed outlier: 3.842A  pdb=" N   ILE R 236 " --> pdb=" O   THR R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 242 through 254
      removed outlier: 4.229A  pdb=" N   ILE R 248 " --> pdb=" O   ARG R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 287
      removed outlier: 3.523A  pdb=" N   VAL R 263 " --> pdb=" O   ASN R 259 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR R 278 " --> pdb=" O   ALA R 274 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE R 282 " --> pdb=" O   THR R 278 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   PHE R 283 " --> pdb=" O   ALA R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 304
    Processing helix  chain 'S' and resid 52 through 56
      removed outlier: 4.044A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186
      removed outlier: 6.355A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.809A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50
      removed outlier: 5.716A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.803A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASP B  83 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.736A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.610A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.232A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.892A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.267A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.591A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.591A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 51
      removed outlier: 6.584A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN S  39 " --> pdb=" O   MET S  93 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.699A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147
    Processing sheet with id=AB7, first strand: chain 'S' and resid 165 through 167

    405 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1426
        1.31 -     1.43: 2494
        1.43 -     1.56: 5115
        1.56 -     1.68: 0
        1.68 -     1.81: 89
  Bond restraints: 9124
  Sorted by residual:
  bond pdb=" C9  7ZQ R 401 "
       pdb=" N2  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.444 -0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" C7  7ZQ R 401 "
       pdb=" N1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.444 -0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" N   ILE A 278 "
       pdb=" CA  ILE A 278 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.031 1.17e-02 7.31e+03 7.16e+00
  bond pdb=" C3  7ZQ R 401 "
       pdb="CL1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.732  1.784 -0.052 2.00e-02 2.50e+03 6.64e+00
  bond pdb=" N   LYS A 277 "
       pdb=" CA  LYS A 277 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.37e+00
  ... (remaining 9119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 11742
        1.20 -     2.40: 479
        2.40 -     3.60: 101
        3.60 -     4.80: 32
        4.80 -     6.00: 15
  Bond angle restraints: 12369
  Sorted by residual:
  angle pdb=" CA  ILE A 278 "
        pdb=" C   ILE A 278 "
        pdb=" O   ILE A 278 "
      ideal   model   delta    sigma   weight residual
     121.17  118.05    3.12 1.06e+00 8.90e-01 8.67e+00
  angle pdb=" CA  TYR S 223 "
        pdb=" CB  TYR S 223 "
        pdb=" CG  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     113.90  108.64    5.26 1.80e+00 3.09e-01 8.54e+00
  angle pdb=" C   GLU A 275 "
        pdb=" N   GLU A 276 "
        pdb=" CA  GLU A 276 "
      ideal   model   delta    sigma   weight residual
     120.44  123.99   -3.55 1.36e+00 5.41e-01 6.81e+00
  angle pdb=" CA  LYS R 301 "
        pdb=" C   LYS R 301 "
        pdb=" O   LYS R 301 "
      ideal   model   delta    sigma   weight residual
     121.00  118.26    2.74 1.05e+00 9.07e-01 6.80e+00
  angle pdb=" CA  LYS A 279 "
        pdb=" C   LYS A 279 "
        pdb=" O   LYS A 279 "
      ideal   model   delta    sigma   weight residual
     120.82  118.16    2.66 1.05e+00 9.07e-01 6.41e+00
  ... (remaining 12364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 4858
       17.41 -    34.83: 441
       34.83 -    52.24: 74
       52.24 -    69.65: 14
       69.65 -    87.06: 3
  Dihedral angle restraints: 5390
    sinusoidal: 2101
      harmonic: 3289
  Sorted by residual:
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.54  -53.54     1      1.00e+01 1.00e-02 3.89e+01
  dihedral pdb=" CA  ASN R  93 "
           pdb=" C   ASN R  93 "
           pdb=" N   MET R  94 "
           pdb=" CA  MET R  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.78   25.22     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  GLU S 222 "
           pdb=" C   GLU S 222 "
           pdb=" N   TYR S 223 "
           pdb=" CA  TYR S 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.14  -24.86     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 5387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 899
       0.034 -    0.068: 344
       0.068 -    0.103: 111
       0.103 -    0.137: 38
       0.137 -    0.171: 10
  Chirality restraints: 1402
  Sorted by residual:
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CG  LEU S   4 "
            pdb=" CB  LEU S   4 "
            pdb=" CD1 LEU S   4 "
            pdb=" CD2 LEU S   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.89e-01
  ... (remaining 1399 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R 166 "    0.041 5.00e-02 4.00e+02   6.28e-02 6.30e+00
        pdb=" N   PRO R 167 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO R 167 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 167 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.66e+00
        pdb=" N   PRO S 224 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  84 "    0.011 2.00e-02 2.50e+03   2.12e-02 4.49e+00
        pdb=" C   ASP R  84 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASP R  84 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE R  85 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 164
        2.66 -     3.22: 8576
        3.22 -     3.78: 14085
        3.78 -     4.34: 18997
        4.34 -     4.90: 31814
  Nonbonded interactions: 73636
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NH2 ARG R 244 "
            pdb=" O2  7ZQ R 401 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.228 3.120
  ... (remaining 73631 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=0.50 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:             1.330
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   9125  Z= 0.195
  Angle     :  0.608   6.003  12371  Z= 0.331
  Chirality :  0.043   0.171   1402
  Planarity :  0.005   0.063   1552
  Dihedral  : 13.570  87.063   3265
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1112
  helix:  1.16 (0.28), residues: 388
  sheet: -1.25 (0.31), residues: 280
  loop : -1.42 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.022   0.002   TYR S 223 
 PHE   0.022   0.001   PHE A 196 
 TRP   0.018   0.001   TRP R 241 
 HIS   0.006   0.001   HIS S 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.20 ( 9124)
  covalent geometry    : angle       0.60806 /  0.33 (12369)
  SS BOND              : bond        0.00534 /  0.28 (    1)
  SS BOND              : angle       1.04510 /  0.57 (    2)
  hydrogen bonds       : bond        0.16210 / 11.03 (  396)
  hydrogen bonds       : angle       7.56333 /  5.30 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7742 (mmpt) cc_final: 0.7473 (mmpt)
REVERT: A  209 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7694 (mtmt)
REVERT: B  213 VAL cc_start: 0.7793 (m) cc_final: 0.7230 (t)
REVERT: R   32 TYR cc_start: 0.7288 (t80) cc_final: 0.6986 (t80)
REVERT: R  116 ILE cc_start: 0.7860 (tp) cc_final: 0.7637 (tp)
REVERT: R  153 TYR cc_start: 0.7838 (m-80) cc_final: 0.7446 (m-80)
REVERT: R  200 PHE cc_start: 0.7064 (m-10) cc_final: 0.6686 (m-80)
REVERT: R  205 ILE cc_start: 0.8009 (tp) cc_final: 0.7779 (tp)
REVERT: R  266 MET cc_start: 0.6197 (ppp) cc_final: 0.5995 (ppp)
REVERT: R  276 LEU cc_start: 0.6846 (tp) cc_final: 0.6646 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1144
  time to fit residues: 30.5284
Evaluate side-chains
  187 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0470
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.6680

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 304 GLN
B 220 GLN
B 230 ASN
B 259 GLN
B 268 ASN
B 340 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.141098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126472 restraints weight = 22590.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.47
r_work: 0.3444 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9125  Z= 0.177
  Angle     :  0.616   7.280  12371  Z= 0.326
  Chirality :  0.043   0.206   1402
  Planarity :  0.005   0.062   1552
  Dihedral  :  5.265  53.933   1232
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.35 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1112
  helix:  1.13 (0.27), residues: 391
  sheet: -1.29 (0.30), residues: 280
  loop : -1.36 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R  58 
 TYR   0.025   0.002   TYR S 223 
 PHE   0.012   0.001   PHE R 303 
 TRP   0.012   0.002   TRP R 241 
 HIS   0.005   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.18 ( 9124)
  covalent geometry    : angle       0.61610 /  0.33 (12369)
  SS BOND              : bond        0.00865 /  0.46 (    1)
  SS BOND              : angle       0.81793 /  0.46 (    2)
  hydrogen bonds       : bond        0.04270 /  2.86 (  396)
  hydrogen bonds       : angle       5.91073 /  4.08 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 209
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7985 (mtmt)
REVERT: B  205 ASP cc_start: 0.7049 (p0) cc_final: 0.6830 (p0)
REVERT: B  213 VAL cc_start: 0.7979 (m) cc_final: 0.7520 (t)
REVERT: R   32 TYR cc_start: 0.7495 (t80) cc_final: 0.7203 (t80)
REVERT: R  116 ILE cc_start: 0.8013 (tp) cc_final: 0.7773 (tp)
REVERT: R  153 TYR cc_start: 0.8018 (m-80) cc_final: 0.7289 (m-80)
REVERT: R  205 ILE cc_start: 0.8183 (tp) cc_final: 0.7960 (tp)
REVERT: R  236 ILE cc_start: 0.7414 (tp) cc_final: 0.6994 (tp)
REVERT: R  266 MET cc_start: 0.6289 (ppp) cc_final: 0.5721 (ppp)
REVERT: S   37 VAL cc_start: 0.8510 (m) cc_final: 0.8192 (t)
REVERT: S   60 TYR cc_start: 0.7434 (m-80) cc_final: 0.7005 (m-80)
REVERT: S   82 GLN cc_start: 0.7641 (tp40) cc_final: 0.7401 (tp40)
REVERT: S  130 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7021 (mt0)
REVERT: S  143 VAL cc_start: 0.8187 (m) cc_final: 0.7908 (p)
REVERT: S  163 TYR cc_start: 0.7378 (m-80) cc_final: 0.7153 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 211
  average time/residue: 0.1030
  time to fit residues: 28.8146
Evaluate side-chains
  205 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 201
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  130 GLN
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0980
   chunk 101 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.141624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128683 restraints weight = 15265.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.87
r_work: 0.3495 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9125  Z= 0.142
  Angle     :  0.578   7.798  12371  Z= 0.303
  Chirality :  0.042   0.200   1402
  Planarity :  0.005   0.060   1552
  Dihedral  :  5.239  57.980   1232
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.40 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.26), residues: 1112
  helix:  1.15 (0.27), residues: 394
  sheet: -1.37 (0.29), residues: 288
  loop : -1.14 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R  58 
 TYR   0.024   0.002   TYR S 223 
 PHE   0.014   0.001   PHE S 108 
 TRP   0.013   0.001   TRP R 241 
 HIS   0.003   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 9124)
  covalent geometry    : angle       0.57825 /  0.30 (12369)
  SS BOND              : bond        0.00598 /  0.31 (    1)
  SS BOND              : angle       0.88658 /  0.49 (    2)
  hydrogen bonds       : bond        0.03779 /  2.52 (  396)
  hydrogen bonds       : angle       5.49196 /  3.79 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8047 (mttm) cc_final: 0.7826 (mttm)
REVERT: A   29 LYS cc_start: 0.7845 (mmpt) cc_final: 0.7550 (mmpt)
REVERT: A   32 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8112 (mtt-85)
REVERT: A  209 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8107 (mtmt)
REVERT: B  101 MET cc_start: 0.7326 (mtp) cc_final: 0.7123 (mtp)
REVERT: B  133 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8130 (m)
REVERT: B  150 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7859 (mpt180)
REVERT: B  205 ASP cc_start: 0.7183 (p0) cc_final: 0.6921 (p0)
REVERT: B  213 VAL cc_start: 0.8024 (m) cc_final: 0.7592 (t)
REVERT: B  247 ASP cc_start: 0.7015 (t0) cc_final: 0.6780 (t0)
REVERT: B  254 ASP cc_start: 0.7139 (t0) cc_final: 0.6887 (t0)
REVERT: R   32 TYR cc_start: 0.7635 (t80) cc_final: 0.7327 (t80)
REVERT: R  205 ILE cc_start: 0.8298 (tp) cc_final: 0.8073 (tp)
REVERT: S   35 HIS cc_start: 0.8535 (m-70) cc_final: 0.8262 (m-70)
REVERT: S   37 VAL cc_start: 0.8617 (m) cc_final: 0.8280 (t)
REVERT: S   82 GLN cc_start: 0.7754 (tp40) cc_final: 0.7470 (tp40)
  outliers start: 16
  outliers final: 8
  residues processed: 204
  average time/residue: 0.1028
  time to fit residues: 27.8245
Evaluate side-chains
  203 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 194
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 259 GLN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.141124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126239 restraints weight = 21431.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.50
r_work: 0.3428 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9125  Z= 0.172
  Angle     :  0.595   7.608  12371  Z= 0.312
  Chirality :  0.043   0.205   1402
  Planarity :  0.005   0.060   1552
  Dihedral  :  5.291  59.162   1232
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.24 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.26), residues: 1112
  helix:  1.07 (0.27), residues: 394
  sheet: -1.32 (0.29), residues: 285
  loop : -1.11 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R  58 
 TYR   0.028   0.002   TYR S 223 
 PHE   0.012   0.001   PHE S 108 
 TRP   0.012   0.002   TRP B 211 
 HIS   0.004   0.001   HIS S 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 ( 9124)
  covalent geometry    : angle       0.59530 /  0.31 (12369)
  SS BOND              : bond        0.00617 /  0.32 (    1)
  SS BOND              : angle       0.30962 /  0.16 (    2)
  hydrogen bonds       : bond        0.03772 /  2.53 (  396)
  hydrogen bonds       : angle       5.35801 /  3.69 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.7775 (mmpt) cc_final: 0.7449 (mmpt)
REVERT: A   32 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.8007 (mtt-85)
REVERT: A  209 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7977 (mtmt)
REVERT: B  133 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8116 (m)
REVERT: B  205 ASP cc_start: 0.7053 (p0) cc_final: 0.6793 (p0)
REVERT: B  213 VAL cc_start: 0.7946 (m) cc_final: 0.7569 (t)
REVERT: B  247 ASP cc_start: 0.6932 (t0) cc_final: 0.6568 (t0)
REVERT: B  254 ASP cc_start: 0.6866 (t0) cc_final: 0.6581 (t0)
REVERT: R  205 ILE cc_start: 0.8199 (tp) cc_final: 0.7970 (tp)
REVERT: R  236 ILE cc_start: 0.7468 (tp) cc_final: 0.7066 (tp)
REVERT: S   35 HIS cc_start: 0.8337 (m-70) cc_final: 0.8083 (m-70)
REVERT: S   82 GLN cc_start: 0.7632 (tp40) cc_final: 0.7334 (tp40)
  outliers start: 20
  outliers final: 14
  residues processed: 213
  average time/residue: 0.1124
  time to fit residues: 31.8690
Evaluate side-chains
  215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.125228 restraints weight = 22891.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.47
r_work: 0.3428 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9125  Z= 0.174
  Angle     :  0.585   7.273  12371  Z= 0.306
  Chirality :  0.042   0.206   1402
  Planarity :  0.005   0.060   1552
  Dihedral  :  5.340  61.942   1232
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.73 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 1112
  helix:  1.06 (0.26), residues: 395
  sheet: -1.27 (0.30), residues: 285
  loop : -1.08 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  58 
 TYR   0.028   0.002   TYR S 223 
 PHE   0.023   0.001   PHE S 108 
 TRP   0.013   0.002   TRP R 241 
 HIS   0.004   0.001   HIS R 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 ( 9124)
  covalent geometry    : angle       0.58495 /  0.31 (12369)
  SS BOND              : bond        0.00559 /  0.29 (    1)
  SS BOND              : angle       0.50512 /  0.27 (    2)
  hydrogen bonds       : bond        0.03704 /  2.48 (  396)
  hydrogen bonds       : angle       5.28752 /  3.64 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 207
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7967 (mtmt)
REVERT: B  133 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8129 (m)
REVERT: B  173 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7908 (p)
REVERT: B  213 VAL cc_start: 0.7949 (m) cc_final: 0.7586 (t)
REVERT: B  228 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7352 (p0)
REVERT: B  247 ASP cc_start: 0.6969 (t0) cc_final: 0.6583 (t0)
REVERT: B  254 ASP cc_start: 0.6844 (t0) cc_final: 0.6556 (t0)
REVERT: R   32 TYR cc_start: 0.7585 (t80) cc_final: 0.7199 (t80)
REVERT: R  116 ILE cc_start: 0.8038 (tp) cc_final: 0.7800 (tp)
REVERT: R  205 ILE cc_start: 0.8222 (tp) cc_final: 0.8006 (tp)
REVERT: R  236 ILE cc_start: 0.7515 (tp) cc_final: 0.7163 (tp)
REVERT: S   35 HIS cc_start: 0.8369 (m-70) cc_final: 0.8111 (m-70)
REVERT: S   82 GLN cc_start: 0.7652 (tp40) cc_final: 0.7378 (tp40)
  outliers start: 28
  outliers final: 20
  residues processed: 219
  average time/residue: 0.1067
  time to fit residues: 31.5204
Evaluate side-chains
  230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    0.0970
   chunk 108 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 340 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.127502 restraints weight = 15233.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.86
r_work: 0.3491 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9125  Z= 0.147
  Angle     :  0.576   7.321  12371  Z= 0.301
  Chirality :  0.041   0.193   1402
  Planarity :  0.004   0.059   1552
  Dihedral  :  5.272  61.866   1232
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.47 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.26), residues: 1112
  helix:  1.14 (0.27), residues: 395
  sheet: -1.22 (0.30), residues: 283
  loop : -1.01 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.027   0.002   TYR S 223 
 PHE   0.018   0.001   PHE S 108 
 TRP   0.013   0.002   TRP B 211 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 9124)
  covalent geometry    : angle       0.57575 /  0.30 (12369)
  SS BOND              : bond        0.00487 /  0.26 (    1)
  SS BOND              : angle       0.48700 /  0.26 (    2)
  hydrogen bonds       : bond        0.03527 /  2.37 (  396)
  hydrogen bonds       : angle       5.16098 /  3.56 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 205
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7503 (m-30) cc_final: 0.7268 (m-30)
REVERT: A   29 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7603 (mmpt)
REVERT: A  209 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8128 (mtmt)
REVERT: B  133 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8168 (m)
REVERT: B  173 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7979 (p)
REVERT: B  197 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7502 (mtm110)
REVERT: B  213 VAL cc_start: 0.7993 (m) cc_final: 0.7599 (t)
REVERT: B  228 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7458 (p0)
REVERT: B  247 ASP cc_start: 0.7070 (t0) cc_final: 0.6805 (t0)
REVERT: B  254 ASP cc_start: 0.7044 (t0) cc_final: 0.6781 (t0)
REVERT: R   32 TYR cc_start: 0.7669 (t80) cc_final: 0.7271 (t80)
REVERT: R  116 ILE cc_start: 0.8118 (tp) cc_final: 0.7890 (tp)
REVERT: R  205 ILE cc_start: 0.8311 (tp) cc_final: 0.8092 (tp)
REVERT: R  236 ILE cc_start: 0.7565 (tp) cc_final: 0.7197 (tp)
REVERT: S   35 HIS cc_start: 0.8362 (m-70) cc_final: 0.8142 (m-70)
REVERT: S   82 GLN cc_start: 0.7728 (tp40) cc_final: 0.7457 (tp40)
REVERT: S  128 MET cc_start: 0.7804 (mtp) cc_final: 0.7568 (mtt)
  outliers start: 26
  outliers final: 19
  residues processed: 216
  average time/residue: 0.1106
  time to fit residues: 32.0184
Evaluate side-chains
  225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  266 MET
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0270
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0370
   chunk 97 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 108 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127435 restraints weight = 15382.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.87
r_work: 0.3489 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9125  Z= 0.147
  Angle     :  0.576   7.303  12371  Z= 0.301
  Chirality :  0.042   0.199   1402
  Planarity :  0.004   0.058   1552
  Dihedral  :  5.238  62.254   1232
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.29 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.26), residues: 1112
  helix:  1.18 (0.27), residues: 395
  sheet: -1.20 (0.30), residues: 283
  loop : -0.99 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.030   0.002   TYR S 223 
 PHE   0.023   0.001   PHE S 108 
 TRP   0.014   0.002   TRP R 241 
 HIS   0.004   0.001   HIS S 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9124)
  covalent geometry    : angle       0.57552 /  0.30 (12369)
  SS BOND              : bond        0.00478 /  0.25 (    1)
  SS BOND              : angle       0.47990 /  0.25 (    2)
  hydrogen bonds       : bond        0.03492 /  2.34 (  396)
  hydrogen bonds       : angle       5.13857 /  3.53 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.7499 (m-30) cc_final: 0.7266 (m-30)
REVERT: A   29 LYS cc_start: 0.7926 (mmpt) cc_final: 0.7583 (mmpt)
REVERT: B  133 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8168 (m)
REVERT: B  173 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (p)
REVERT: B  197 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7447 (mtm110)
REVERT: B  228 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7398 (p0)
REVERT: B  247 ASP cc_start: 0.7085 (t0) cc_final: 0.6684 (t0)
REVERT: B  254 ASP cc_start: 0.7045 (t0) cc_final: 0.6791 (t0)
REVERT: R   32 TYR cc_start: 0.7686 (t80) cc_final: 0.7278 (t80)
REVERT: R  116 ILE cc_start: 0.8121 (tp) cc_final: 0.7889 (tp)
REVERT: R  205 ILE cc_start: 0.8313 (tp) cc_final: 0.8099 (tp)
REVERT: R  236 ILE cc_start: 0.7502 (tp) cc_final: 0.7160 (tp)
REVERT: S   35 HIS cc_start: 0.8386 (m-70) cc_final: 0.8108 (m-70)
REVERT: S   53 SER cc_start: 0.7876 (m) cc_final: 0.7634 (m)
  outliers start: 25
  outliers final: 22
  residues processed: 216
  average time/residue: 0.1098
  time to fit residues: 31.8414
Evaluate side-chains
  222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue  266 MET
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 155 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.124822 restraints weight = 27155.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.79
r_work: 0.3412 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9125  Z= 0.161
  Angle     :  0.587   7.851  12371  Z= 0.306
  Chirality :  0.042   0.205   1402
  Planarity :  0.004   0.058   1552
  Dihedral  :  5.277  62.488   1232
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.88 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.26), residues: 1112
  helix:  1.20 (0.26), residues: 397
  sheet: -1.26 (0.29), residues: 285
  loop : -0.99 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  32 
 TYR   0.030   0.002   TYR S 223 
 PHE   0.020   0.001   PHE S 108 
 TRP   0.013   0.002   TRP R 241 
 HIS   0.004   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 9124)
  covalent geometry    : angle       0.58730 /  0.31 (12369)
  SS BOND              : bond        0.00445 /  0.23 (    1)
  SS BOND              : angle       0.47806 /  0.25 (    2)
  hydrogen bonds       : bond        0.03550 /  2.38 (  396)
  hydrogen bonds       : angle       5.12637 /  3.52 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7399 (m-30) cc_final: 0.7159 (m-30)
REVERT: A   29 LYS cc_start: 0.7859 (mmpt) cc_final: 0.7499 (mmpt)
REVERT: A  243 MET cc_start: 0.6135 (mtp) cc_final: 0.5883 (mmm)
REVERT: B  133 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (m)
REVERT: B  173 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7941 (p)
REVERT: B  197 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7306 (mtm110)
REVERT: B  228 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7314 (p0)
REVERT: B  247 ASP cc_start: 0.6974 (t0) cc_final: 0.6582 (t0)
REVERT: B  254 ASP cc_start: 0.6923 (t0) cc_final: 0.6673 (t0)
REVERT: B  312 ASP cc_start: 0.7603 (t0) cc_final: 0.7311 (t0)
REVERT: R   32 TYR cc_start: 0.7642 (t80) cc_final: 0.7254 (t80)
REVERT: R  116 ILE cc_start: 0.8061 (tp) cc_final: 0.7825 (tp)
REVERT: R  205 ILE cc_start: 0.8242 (tp) cc_final: 0.8017 (tp)
REVERT: R  236 ILE cc_start: 0.7496 (tp) cc_final: 0.7121 (tp)
REVERT: S   35 HIS cc_start: 0.8301 (m-70) cc_final: 0.8079 (m-70)
REVERT: S   53 SER cc_start: 0.7810 (m) cc_final: 0.7570 (m)
  outliers start: 31
  outliers final: 26
  residues processed: 213
  average time/residue: 0.1116
  time to fit residues: 31.8253
Evaluate side-chains
  227 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue  266 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0270
   chunk 64 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126747 restraints weight = 17998.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.10
r_work: 0.3470 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9125  Z= 0.151
  Angle     :  0.587   7.470  12371  Z= 0.305
  Chirality :  0.042   0.206   1402
  Planarity :  0.004   0.058   1552
  Dihedral  :  5.241  62.529   1232
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.70 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.26), residues: 1112
  helix:  1.26 (0.27), residues: 396
  sheet: -1.29 (0.29), residues: 285
  loop : -1.00 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.031   0.002   TYR S 223 
 PHE   0.019   0.001   PHE S 108 
 TRP   0.014   0.002   TRP R 241 
 HIS   0.004   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 9124)
  covalent geometry    : angle       0.58726 /  0.30 (12369)
  SS BOND              : bond        0.00402 /  0.21 (    1)
  SS BOND              : angle       0.48004 /  0.25 (    2)
  hydrogen bonds       : bond        0.03474 /  2.33 (  396)
  hydrogen bonds       : angle       5.10877 /  3.51 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 200
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7922 (mmpt) cc_final: 0.7572 (mmpt)
REVERT: A  243 MET cc_start: 0.6187 (mtp) cc_final: 0.5970 (mmm)
REVERT: B   70 LEU cc_start: 0.8261 (mt) cc_final: 0.7992 (tp)
REVERT: B  133 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8190 (m)
REVERT: B  173 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (p)
REVERT: B  197 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7482 (mtm110)
REVERT: B  228 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7512 (p0)
REVERT: B  247 ASP cc_start: 0.7140 (t0) cc_final: 0.6718 (t0)
REVERT: B  254 ASP cc_start: 0.7115 (t0) cc_final: 0.6876 (t0)
REVERT: B  308 LEU cc_start: 0.8199 (mt) cc_final: 0.7963 (mp)
REVERT: B  312 ASP cc_start: 0.7798 (t0) cc_final: 0.7515 (t0)
REVERT: R   32 TYR cc_start: 0.7700 (t80) cc_final: 0.7303 (t80)
REVERT: R  116 ILE cc_start: 0.8157 (tp) cc_final: 0.7929 (tp)
REVERT: R  205 ILE cc_start: 0.8357 (tp) cc_final: 0.8141 (tp)
REVERT: S   53 SER cc_start: 0.7897 (m) cc_final: 0.7645 (m)
  outliers start: 29
  outliers final: 26
  residues processed: 216
  average time/residue: 0.1133
  time to fit residues: 32.7144
Evaluate side-chains
  223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue  266 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 89 optimal weight:    0.6980
   chunk 105 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0470
   chunk 73 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.141574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.128531 restraints weight = 15270.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.87
r_work: 0.3493 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9125  Z= 0.137
  Angle     :  0.586   7.371  12371  Z= 0.303
  Chirality :  0.042   0.199   1402
  Planarity :  0.004   0.057   1552
  Dihedral  :  5.226  63.190   1232
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.21 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.26), residues: 1112
  helix:  1.32 (0.27), residues: 396
  sheet: -1.33 (0.29), residues: 285
  loop : -0.96 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.029   0.002   TYR S 223 
 PHE   0.021   0.001   PHE S 108 
 TRP   0.016   0.001   TRP R 241 
 HIS   0.007   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 9124)
  covalent geometry    : angle       0.58561 /  0.30 (12369)
  SS BOND              : bond        0.00379 /  0.20 (    1)
  SS BOND              : angle       0.87004 /  0.46 (    2)
  hydrogen bonds       : bond        0.03392 /  2.28 (  396)
  hydrogen bonds       : angle       5.06520 /  3.48 ( 1143)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7508 (m-30) cc_final: 0.7274 (m-30)
REVERT: A   29 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7528 (mmpt)
REVERT: B   70 LEU cc_start: 0.8239 (mt) cc_final: 0.7977 (tp)
REVERT: B  173 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7948 (p)
REVERT: B  197 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7492 (mtm110)
REVERT: B  228 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7274 (p0)
REVERT: B  247 ASP cc_start: 0.6972 (t0) cc_final: 0.6636 (t0)
REVERT: B  254 ASP cc_start: 0.7067 (t0) cc_final: 0.6829 (t0)
REVERT: B  312 ASP cc_start: 0.7711 (t0) cc_final: 0.7433 (t0)
REVERT: R   32 TYR cc_start: 0.7674 (t80) cc_final: 0.7275 (t80)
REVERT: R   69 LEU cc_start: 0.8252 (tp) cc_final: 0.7992 (tp)
REVERT: R  116 ILE cc_start: 0.8110 (tp) cc_final: 0.7886 (tp)
REVERT: R  205 ILE cc_start: 0.8304 (tp) cc_final: 0.8089 (tp)
REVERT: R  236 ILE cc_start: 0.7518 (tp) cc_final: 0.7156 (tp)
REVERT: S   53 SER cc_start: 0.7780 (m) cc_final: 0.7523 (m)
REVERT: S  143 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (p)
  outliers start: 27
  outliers final: 24
  residues processed: 210
  average time/residue: 0.1124
  time to fit residues: 31.4905
Evaluate side-chains
  219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue  266 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   37 VAL
Chi-restraints excluded: chain S residue  120 SER
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    0.0030
   chunk 82 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0030
   chunk 58 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.3200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.142983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.128461 restraints weight = 21318.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.39
r_work: 0.3473 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3475
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9125  Z= 0.117
  Angle     :  0.567   7.639  12371  Z= 0.292
  Chirality :  0.041   0.190   1402
  Planarity :  0.004   0.057   1552
  Dihedral  :  5.092  62.242   1232
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.93 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.26), residues: 1112
  helix:  1.42 (0.27), residues: 395
  sheet: -1.30 (0.29), residues: 285
  loop : -0.94 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.024   0.001   TYR S 223 
 PHE   0.019   0.001   PHE S 108 
 TRP   0.016   0.001   TRP R 241 
 HIS   0.006   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 9124)
  covalent geometry    : angle       0.56671 /  0.29 (12369)
  SS BOND              : bond        0.00499 /  0.26 (    1)
  SS BOND              : angle       0.70409 /  0.38 (    2)
  hydrogen bonds       : bond        0.03217 /  2.15 (  396)
  hydrogen bonds       : angle       4.97726 /  3.42 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2524.33 seconds
wall clock time: 44 minutes 13.74 seconds (2653.74 seconds total)