Starting phenix.real_space_refine
on Tue Mar  3 23:42:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2026/7vui_32129.cif"
  }
  resolution = 3.3
  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=   0.023
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: 7
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      49      5.16       5
     Cl      1      4.86       5
     C    5274      2.51       5
     N    1433      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8287
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1940
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2295
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 12, 'TRANS': 266}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 1.69, per 1000 atoms: 0.20
  Number of scatterers: 8287
  At special positions: 0
  Unit cell: (76.96, 98.8, 134.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      49     16.00
     P       3     15.00
     Mg      1     11.99
     O    1526      8.00
     N    1433      7.00
     C    5274      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 309.0 milliseconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      41.5% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 3.795A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.669A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.147A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 3.797A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.875A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.595A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 53
      removed outlier: 3.973A  pdb=" N   SER R  34 " --> pdb=" O   VAL R  30 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU R  35 " --> pdb=" O   VAL R  31 " (cutoff:3.500A)
      Proline residue:  R  42  - end of helix
      removed outlier: 3.706A  pdb=" N   GLN R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 58
      removed outlier: 3.887A  pdb=" N   ARG R  58 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 82
      removed outlier: 3.574A  pdb=" N   TYR R  65 " --> pdb=" O   SER R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 91
      removed outlier: 5.342A  pdb=" N   ASP R  89 " --> pdb=" O   PHE R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 132
      removed outlier: 3.861A  pdb=" N   VAL R 106 " --> pdb=" O   LYS R 102 " (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: 3.560A  pdb=" N   LYS R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL R 152 " --> pdb=" O   VAL R 148 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   TYR R 153 " --> pdb=" O   ILE R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 166
      removed outlier: 3.655A  pdb=" N   TRP R 165 " --> pdb=" O   PRO R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 192
      removed outlier: 3.873A  pdb=" N   HIS R 181 " --> pdb=" O   THR R 177 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL R 182 " --> pdb=" O   SER R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 213
    Processing helix  chain 'R' and resid 222 through 253
      Proline residue:  R 243  - end of helix
    Processing helix  chain 'R' and resid 259 through 286
      removed outlier: 4.087A  pdb=" N   MET R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER R 267 " --> pdb=" O   VAL R 263 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU R 273 " --> pdb=" O   ILE R 269 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ALA R 274 " --> pdb=" O   ALA R 270 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU R 275 " --> pdb=" O   ASN R 271 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   PHE R 282 " --> pdb=" O   THR R 278 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   PHE R 283 " --> pdb=" O   ALA R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 301
      removed outlier: 3.740A  pdb=" N   MET R 295 " --> pdb=" O   ARG R 291 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS R 301 " --> pdb=" O   ALA R 297 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.517A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   MET A 221 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.035A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63
      removed outlier: 3.540A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.537A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.597A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.702A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.656A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.532A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.803A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60
      removed outlier: 6.680A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1104 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: 1.31

  Time building geometry restraints manager: 0.86 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: 1328
        1.31 -     1.44: 2379
        1.44 -     1.56: 4686
        1.56 -     1.69: 5
        1.69 -     1.81: 70
  Bond restraints: 8468
  Sorted by residual:
  bond pdb=" C9  7ZQ R 401 "
       pdb=" N2  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.450 -0.109 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" C7  7ZQ R 401 "
       pdb=" N1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.450 -0.106 2.00e-02 2.50e+03 2.80e+01
  bond pdb=" C2  GTP A 401 "
       pdb=" N3  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.380  1.321  0.059 2.00e-02 2.50e+03 8.61e+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 6.88e+00
  bond pdb=" C8  GTP A 401 "
       pdb=" N7  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.300  0.050 2.00e-02 2.50e+03 6.24e+00
  ... (remaining 8463 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 11264
        1.81 -     3.62: 177
        3.62 -     5.43: 32
        5.43 -     7.25: 12
        7.25 -     9.06: 7
  Bond angle restraints: 11492
  Sorted by residual:
  angle pdb=" C4  GTP A 401 "
        pdb=" N9  GTP A 401 "
        pdb=" C8  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     108.00  117.06   -9.06 3.00e+00 1.11e-01 9.11e+00
  angle pdb=" CB  ARG A 270 "
        pdb=" CG  ARG A 270 "
        pdb=" CD  ARG A 270 "
      ideal   model   delta    sigma   weight residual
     111.30  118.16   -6.86 2.30e+00 1.89e-01 8.88e+00
  angle pdb=" C5  GTP A 401 "
        pdb=" C4  GTP A 401 "
        pdb=" N9  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     108.00   99.48    8.52 3.00e+00 1.11e-01 8.07e+00
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  101.13    8.37 3.00e+00 1.11e-01 7.78e+00
  angle pdb=" O1A GTP A 401 "
        pdb=" PA  GTP A 401 "
        pdb=" O2A GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  101.18    8.32 3.00e+00 1.11e-01 7.69e+00
  ... (remaining 11487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.60: 4927
       33.60 -    67.20: 89
       67.20 -   100.81: 13
      100.81 -   134.41: 2
      134.41 -   168.01: 3
  Dihedral angle restraints: 5034
    sinusoidal: 2005
      harmonic: 3029
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -6.48  -79.52     1      1.00e+01 1.00e-02 7.85e+01
  dihedral pdb=" O2G GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PG  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -14.69 -168.01     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -49.86  154.45     1      2.00e+01 2.50e-03 4.57e+01
  ... (remaining 5031 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 893
       0.038 -    0.076: 297
       0.076 -    0.114: 88
       0.114 -    0.152: 13
       0.152 -    0.190: 4
  Chirality restraints: 1295
  Sorted by residual:
  chirality pdb=" C3' GTP A 401 "
            pdb=" C2' GTP A 401 "
            pdb=" C4' GTP A 401 "
            pdb=" O3' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.66    0.19 2.00e-01 2.50e+01 9.03e-01
  chirality pdb=" C10 7ZQ R 401 "
            pdb=" C11 7ZQ R 401 "
            pdb=" C12 7ZQ R 401 "
            pdb=" N2  7ZQ R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.62    0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" C4' GTP A 401 "
            pdb=" C3' GTP A 401 "
            pdb=" C5' GTP A 401 "
            pdb=" O4' GTP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.63    0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 1292 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R  80 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" C   ILE R  80 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE R  80 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL R  81 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  82 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" C   PHE R  82 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PHE R  82 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL R  83 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 321 "    0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO A 322 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 257
        2.71 -     3.26: 8379
        3.26 -     3.81: 13443
        3.81 -     4.35: 16385
        4.35 -     4.90: 27938
  Nonbonded interactions: 66402
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OH  TYR A 308 "
            pdb=" OD2 ASP A 333 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O2G GTP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     2.179 2.170
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.181 3.040
  ... (remaining 66397 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8470  Z= 0.162
  Angle     :  0.628   9.057  11496  Z= 0.306
  Chirality :  0.042   0.190   1295
  Planarity :  0.004   0.047   1452
  Dihedral  : 14.880 168.009   3068
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.11 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -0.34 (0.27), residues: 1022
  helix:  1.06 (0.27), residues: 400
  sheet: -0.97 (0.36), residues: 215
  loop : -1.00 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 270 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.017   0.001   PHE R 287 
 TRP   0.026   0.001   TRP R 170 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8468)
  covalent geometry    : angle       0.62813 (11492)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       0.50142 (    4)
  hydrogen bonds       : bond        0.17414 (  384)
  hydrogen bonds       : angle       6.36338 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.6845 (tmm160) cc_final: 0.5875 (tmm160)
REVERT: A  270 ARG cc_start: 0.6386 (ppt170) cc_final: 0.6171 (ppt170)
REVERT: A  289 GLU cc_start: 0.7270 (tp30) cc_final: 0.6706 (tp30)
REVERT: A  309 THR cc_start: 0.7900 (p) cc_final: 0.7698 (t)
REVERT: A  317 GLU cc_start: 0.6478 (mp0) cc_final: 0.6091 (mp0)
REVERT: A  371 ASP cc_start: 0.7313 (t70) cc_final: 0.6717 (t0)
REVERT: B   66 ASP cc_start: 0.7062 (p0) cc_final: 0.6724 (p0)
REVERT: B   67 SER cc_start: 0.8411 (m) cc_final: 0.7871 (t)
REVERT: B  103 CYS cc_start: 0.7243 (m) cc_final: 0.6816 (m)
REVERT: B  121 CYS cc_start: 0.7334 (t) cc_final: 0.6837 (t)
REVERT: B  155 ASN cc_start: 0.7740 (t0) cc_final: 0.7236 (t0)
REVERT: B  169 TRP cc_start: 0.8099 (m100) cc_final: 0.7657 (m100)
REVERT: B  212 ASP cc_start: 0.7515 (t0) cc_final: 0.7293 (t70)
REVERT: B  256 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7634 (ptp-110)
REVERT: B  258 ASP cc_start: 0.7495 (t70) cc_final: 0.6828 (t0)
REVERT: B  273 ILE cc_start: 0.8184 (mp) cc_final: 0.7878 (mp)
REVERT: G   28 ILE cc_start: 0.8119 (mp) cc_final: 0.7866 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1168
  time to fit residues: 32.9453
Evaluate side-chains
  194 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 377 ASN
B 119 ASN
B 239 ASN
N  53 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.149636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.131228 restraints weight = 11872.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.20
r_work: 0.3562 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8470  Z= 0.173
  Angle     :  0.621   8.646  11496  Z= 0.318
  Chirality :  0.044   0.175   1295
  Planarity :  0.004   0.053   1452
  Dihedral  : 10.076 149.584   1161
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.11 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.50 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.27), residues: 1022
  helix:  1.08 (0.27), residues: 399
  sheet: -0.62 (0.36), residues: 217
  loop : -1.00 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.022   0.002   PHE R  82 
 TRP   0.027   0.002   TRP R 170 
 HIS   0.008   0.002   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8468)
  covalent geometry    : angle       0.62033 (11492)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       1.31987 (    4)
  hydrogen bonds       : bond        0.04562 (  384)
  hydrogen bonds       : angle       5.04980 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7923 (ttmm)
REVERT: A  289 GLU cc_start: 0.7968 (tp30) cc_final: 0.7351 (tp30)
REVERT: A  317 GLU cc_start: 0.6671 (mp0) cc_final: 0.6075 (mp0)
REVERT: A  366 PHE cc_start: 0.7997 (t80) cc_final: 0.7657 (t80)
REVERT: A  371 ASP cc_start: 0.8163 (t70) cc_final: 0.7736 (t0)
REVERT: B   67 SER cc_start: 0.8785 (m) cc_final: 0.8381 (t)
REVERT: B  103 CYS cc_start: 0.7843 (m) cc_final: 0.7400 (m)
REVERT: B  121 CYS cc_start: 0.8031 (t) cc_final: 0.7735 (t)
REVERT: B  169 TRP cc_start: 0.8475 (m100) cc_final: 0.8068 (m100)
REVERT: B  212 ASP cc_start: 0.8188 (t0) cc_final: 0.7975 (t0)
REVERT: B  220 GLN cc_start: 0.7967 (pt0) cc_final: 0.7713 (pt0)
REVERT: B  258 ASP cc_start: 0.8107 (t70) cc_final: 0.7573 (t0)
REVERT: B  259 GLN cc_start: 0.8441 (tt0) cc_final: 0.8139 (tt0)
REVERT: B  304 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7916 (ttm-80)
REVERT: R  239 THR cc_start: 0.7968 (p) cc_final: 0.7736 (t)
  outliers start: 16
  outliers final: 11
  residues processed: 212
  average time/residue: 0.1164
  time to fit residues: 31.4648
Evaluate side-chains
  216 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 205
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  252 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 56 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0170
   chunk 12 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
A 282 ASN
A 377 ASN
N  53 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.146980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.128369 restraints weight = 11767.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.19
r_work: 0.3543 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8470  Z= 0.142
  Angle     :  0.566   7.462  11496  Z= 0.294
  Chirality :  0.043   0.158   1295
  Planarity :  0.004   0.050   1452
  Dihedral  :  9.847 147.639   1161
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.62 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.74 %
    Favored  : 82.14 %
  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: -0.14 (0.27), residues: 1022
  helix:  1.19 (0.27), residues: 399
  sheet: -0.48 (0.35), residues: 226
  loop : -1.13 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.018   0.001   PHE R  82 
 TRP   0.016   0.001   TRP R 170 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8468)
  covalent geometry    : angle       0.56565 (11492)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.87846 (    4)
  hydrogen bonds       : bond        0.04172 (  384)
  hydrogen bonds       : angle       4.84352 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7917 (ttmm)
REVERT: A  289 GLU cc_start: 0.7991 (tp30) cc_final: 0.7385 (tp30)
REVERT: A  317 GLU cc_start: 0.6737 (mp0) cc_final: 0.6160 (mp0)
REVERT: A  346 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7892 (mtt-85)
REVERT: A  366 PHE cc_start: 0.8028 (t80) cc_final: 0.7546 (t80)
REVERT: A  371 ASP cc_start: 0.8183 (t70) cc_final: 0.7689 (t0)
REVERT: B   49 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7591 (mtt90)
REVERT: B   67 SER cc_start: 0.8778 (m) cc_final: 0.8392 (t)
REVERT: B  103 CYS cc_start: 0.7798 (m) cc_final: 0.7392 (m)
REVERT: B  169 TRP cc_start: 0.8503 (m100) cc_final: 0.8095 (m100)
REVERT: B  220 GLN cc_start: 0.7998 (pt0) cc_final: 0.7703 (pt0)
REVERT: B  258 ASP cc_start: 0.8078 (t70) cc_final: 0.7519 (t0)
REVERT: B  304 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7881 (ttm-80)
REVERT: R  239 THR cc_start: 0.7972 (p) cc_final: 0.7751 (t)
  outliers start: 19
  outliers final: 15
  residues processed: 219
  average time/residue: 0.1187
  time to fit residues: 33.2248
Evaluate side-chains
  221 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 206
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  252 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 377 ASN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127666 restraints weight = 12168.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.27
r_work: 0.3506 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8470  Z= 0.164
  Angle     :  0.575   7.383  11496  Z= 0.298
  Chirality :  0.043   0.151   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.650 145.685   1161
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.62 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.31 %
    Favored  : 77.79 %
  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: -0.13 (0.27), residues: 1022
  helix:  1.17 (0.27), residues: 401
  sheet: -0.36 (0.36), residues: 226
  loop : -1.17 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.017   0.001   TYR R  32 
 PHE   0.022   0.001   PHE R  82 
 TRP   0.018   0.001   TRP R 170 
 HIS   0.005   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8468)
  covalent geometry    : angle       0.57474 (11492)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       0.93985 (    4)
  hydrogen bonds       : bond        0.04206 (  384)
  hydrogen bonds       : angle       4.81208 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7819 (ttmm)
REVERT: A  289 GLU cc_start: 0.8001 (tp30) cc_final: 0.7354 (tp30)
REVERT: A  317 GLU cc_start: 0.6769 (mp0) cc_final: 0.6203 (mp0)
REVERT: A  346 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7710 (mtt-85)
REVERT: A  371 ASP cc_start: 0.8179 (t70) cc_final: 0.7724 (t70)
REVERT: B   49 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7596 (mtt90)
REVERT: B   67 SER cc_start: 0.8789 (m) cc_final: 0.8369 (t)
REVERT: B  103 CYS cc_start: 0.7799 (m) cc_final: 0.7324 (m)
REVERT: B  121 CYS cc_start: 0.8013 (t) cc_final: 0.7608 (t)
REVERT: B  169 TRP cc_start: 0.8604 (m100) cc_final: 0.8125 (m100)
REVERT: B  220 GLN cc_start: 0.7951 (pt0) cc_final: 0.7584 (pt0)
REVERT: B  223 THR cc_start: 0.7857 (m) cc_final: 0.7566 (p)
REVERT: B  258 ASP cc_start: 0.8113 (t70) cc_final: 0.7438 (t0)
REVERT: B  259 GLN cc_start: 0.8503 (tt0) cc_final: 0.8256 (tt0)
REVERT: R  199 PHE cc_start: 0.6916 (m-10) cc_final: 0.6513 (m-80)
REVERT: R  239 THR cc_start: 0.7977 (p) cc_final: 0.7758 (t)
  outliers start: 26
  outliers final: 14
  residues processed: 216
  average time/residue: 0.1168
  time to fit residues: 32.1807
Evaluate side-chains
  216 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  252 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0070
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
A 268 ASN
A 282 ASN
A 377 ASN
N  53 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.148466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.129123 restraints weight = 12044.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.27
r_work: 0.3526 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8470  Z= 0.129
  Angle     :  0.557   6.661  11496  Z= 0.288
  Chirality :  0.042   0.149   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.491 144.700   1161
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.52 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.42 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.27), residues: 1022
  helix:  1.28 (0.27), residues: 401
  sheet: -0.17 (0.37), residues: 220
  loop : -1.19 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.019   0.001   TYR R  32 
 PHE   0.025   0.001   PHE R  82 
 TRP   0.020   0.001   TRP R 170 
 HIS   0.009   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8468)
  covalent geometry    : angle       0.55726 (11492)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.75803 (    4)
  hydrogen bonds       : bond        0.03926 (  384)
  hydrogen bonds       : angle       4.72551 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.8507 (t160) cc_final: 0.8300 (t0)
REVERT: A  264 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7803 (ttmm)
REVERT: A  289 GLU cc_start: 0.8010 (tp30) cc_final: 0.7367 (tp30)
REVERT: A  317 GLU cc_start: 0.6815 (mp0) cc_final: 0.6250 (mp0)
REVERT: A  346 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7945 (mtt-85)
REVERT: A  364 ARG cc_start: 0.8362 (mtt90) cc_final: 0.8107 (mtt-85)
REVERT: A  366 PHE cc_start: 0.7936 (t80) cc_final: 0.6923 (t80)
REVERT: A  371 ASP cc_start: 0.8191 (t70) cc_final: 0.7893 (t0)
REVERT: B   49 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7578 (mtt90)
REVERT: B   67 SER cc_start: 0.8771 (m) cc_final: 0.8349 (t)
REVERT: B  103 CYS cc_start: 0.7693 (m) cc_final: 0.7253 (m)
REVERT: B  169 TRP cc_start: 0.8598 (m100) cc_final: 0.8081 (m100)
REVERT: B  220 GLN cc_start: 0.7988 (pt0) cc_final: 0.7628 (pt0)
REVERT: B  223 THR cc_start: 0.7766 (m) cc_final: 0.7519 (p)
REVERT: B  258 ASP cc_start: 0.8099 (t70) cc_final: 0.7442 (t0)
REVERT: B  259 GLN cc_start: 0.8502 (tt0) cc_final: 0.8267 (tt0)
REVERT: R   65 TYR cc_start: 0.8029 (m-80) cc_final: 0.7515 (m-80)
REVERT: R  239 THR cc_start: 0.7978 (p) cc_final: 0.7754 (t)
  outliers start: 23
  outliers final: 18
  residues processed: 213
  average time/residue: 0.1245
  time to fit residues: 33.7708
Evaluate side-chains
  220 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 282 ASN
A 377 ASN
N  53 GLN
R 277 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.145170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.125964 restraints weight = 11994.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.19
r_work: 0.3513 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8470  Z= 0.176
  Angle     :  0.598   6.902  11496  Z= 0.305
  Chirality :  0.044   0.153   1295
  Planarity :  0.004   0.054   1452
  Dihedral  :  9.481 143.177   1161
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.82 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.31 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.27), residues: 1022
  helix:  1.20 (0.27), residues: 401
  sheet: -0.17 (0.36), residues: 223
  loop : -1.17 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.020   0.001   TYR R  32 
 PHE   0.027   0.002   PHE R 199 
 TRP   0.022   0.002   TRP R 170 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8468)
  covalent geometry    : angle       0.59822 (11492)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.86950 (    4)
  hydrogen bonds       : bond        0.04212 (  384)
  hydrogen bonds       : angle       4.77131 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 204
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7813 (ttmm)
REVERT: A  289 GLU cc_start: 0.8034 (tp30) cc_final: 0.7403 (tp30)
REVERT: A  309 THR cc_start: 0.8162 (t) cc_final: 0.7895 (p)
REVERT: A  317 GLU cc_start: 0.6909 (mp0) cc_final: 0.6346 (mp0)
REVERT: A  364 ARG cc_start: 0.8362 (mtt90) cc_final: 0.8128 (mtt-85)
REVERT: A  366 PHE cc_start: 0.7961 (t80) cc_final: 0.6961 (t80)
REVERT: A  371 ASP cc_start: 0.8195 (t70) cc_final: 0.7671 (t70)
REVERT: B   49 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7647 (mtt90)
REVERT: B   67 SER cc_start: 0.8806 (m) cc_final: 0.8364 (t)
REVERT: B  103 CYS cc_start: 0.7729 (m) cc_final: 0.7242 (m)
REVERT: B  121 CYS cc_start: 0.7982 (t) cc_final: 0.7590 (t)
REVERT: B  169 TRP cc_start: 0.8617 (m100) cc_final: 0.8125 (m100)
REVERT: B  220 GLN cc_start: 0.8011 (pt0) cc_final: 0.7659 (pt0)
REVERT: B  223 THR cc_start: 0.7808 (m) cc_final: 0.7578 (p)
REVERT: B  258 ASP cc_start: 0.8024 (t70) cc_final: 0.7339 (t0)
REVERT: B  259 GLN cc_start: 0.8569 (tt0) cc_final: 0.8366 (tt0)
REVERT: G   28 ILE cc_start: 0.8066 (mp) cc_final: 0.7821 (mp)
REVERT: R   65 TYR cc_start: 0.8057 (m-80) cc_final: 0.7549 (m-80)
  outliers start: 34
  outliers final: 23
  residues processed: 226
  average time/residue: 0.1136
  time to fit residues: 32.9091
Evaluate side-chains
  231 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0870
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0060
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 99 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.3374

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 282 ASN
A 377 ASN
N  53 GLN
R 277 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129680 restraints weight = 12054.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.26
r_work: 0.3530 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8470  Z= 0.122
  Angle     :  0.575   6.802  11496  Z= 0.294
  Chirality :  0.042   0.147   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.319 143.025   1161
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.52 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.32 %
    Favored  : 75.22 %
  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:  0.13 (0.27), residues: 1022
  helix:  1.42 (0.27), residues: 394
  sheet: -0.07 (0.37), residues: 217
  loop : -1.13 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.021   0.001   TYR R  32 
 PHE   0.021   0.001   PHE R 199 
 TRP   0.023   0.001   TRP R 170 
 HIS   0.008   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8468)
  covalent geometry    : angle       0.57531 (11492)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.76685 (    4)
  hydrogen bonds       : bond        0.03831 (  384)
  hydrogen bonds       : angle       4.66782 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 207
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7807 (ttmm)
REVERT: A  289 GLU cc_start: 0.7986 (tp30) cc_final: 0.7334 (tp30)
REVERT: A  317 GLU cc_start: 0.6855 (mp0) cc_final: 0.6277 (mp0)
REVERT: A  346 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7634 (mtt-85)
REVERT: A  366 PHE cc_start: 0.7893 (t80) cc_final: 0.6915 (t80)
REVERT: A  371 ASP cc_start: 0.8199 (t70) cc_final: 0.7938 (t0)
REVERT: B   49 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7610 (mtt90)
REVERT: B   67 SER cc_start: 0.8770 (m) cc_final: 0.8307 (t)
REVERT: B  103 CYS cc_start: 0.7746 (m) cc_final: 0.7287 (m)
REVERT: B  169 TRP cc_start: 0.8619 (m100) cc_final: 0.8136 (m100)
REVERT: B  220 GLN cc_start: 0.7924 (pt0) cc_final: 0.7596 (pt0)
REVERT: B  223 THR cc_start: 0.7706 (m) cc_final: 0.7480 (p)
REVERT: B  258 ASP cc_start: 0.8034 (t70) cc_final: 0.7356 (t0)
REVERT: R   65 TYR cc_start: 0.8015 (m-80) cc_final: 0.7485 (m-80)
  outliers start: 31
  outliers final: 22
  residues processed: 227
  average time/residue: 0.1178
  time to fit residues: 34.2671
Evaluate side-chains
  228 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 206
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  282 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 92 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 282 ASN
A 377 ASN
B 239 ASN
N  53 GLN
R 277 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.146856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.127765 restraints weight = 11974.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.24
r_work: 0.3498 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8470  Z= 0.177
  Angle     :  0.610   7.490  11496  Z= 0.313
  Chirality :  0.044   0.154   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.318 141.861   1161
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.82 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.10 %
    Favored  : 74.33 %
  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:  0.02 (0.27), residues: 1022
  helix:  1.31 (0.27), residues: 394
  sheet: -0.09 (0.37), residues: 217
  loop : -1.18 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.019   0.001   TYR R  32 
 PHE   0.019   0.001   PHE R 199 
 TRP   0.026   0.002   TRP R 170 
 HIS   0.010   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8468)
  covalent geometry    : angle       0.61008 (11492)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.86143 (    4)
  hydrogen bonds       : bond        0.04201 (  384)
  hydrogen bonds       : angle       4.73803 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7782 (ttmm)
REVERT: A  289 GLU cc_start: 0.7992 (tp30) cc_final: 0.7349 (tp30)
REVERT: A  317 GLU cc_start: 0.6961 (mp0) cc_final: 0.6395 (mp0)
REVERT: A  346 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7612 (mtt-85)
REVERT: A  364 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8209 (mtt-85)
REVERT: A  371 ASP cc_start: 0.8230 (t70) cc_final: 0.7921 (t0)
REVERT: B   49 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7703 (mtt90)
REVERT: B   67 SER cc_start: 0.8820 (m) cc_final: 0.8374 (t)
REVERT: B  103 CYS cc_start: 0.7754 (m) cc_final: 0.7259 (m)
REVERT: B  121 CYS cc_start: 0.8034 (t) cc_final: 0.7656 (t)
REVERT: B  169 TRP cc_start: 0.8621 (m100) cc_final: 0.8144 (m100)
REVERT: B  220 GLN cc_start: 0.7977 (pt0) cc_final: 0.7611 (pt0)
REVERT: B  223 THR cc_start: 0.7817 (m) cc_final: 0.7601 (p)
REVERT: B  256 ARG cc_start: 0.8231 (ptp-110) cc_final: 0.7993 (ptp-110)
REVERT: B  258 ASP cc_start: 0.8114 (t70) cc_final: 0.7364 (t0)
REVERT: B  259 GLN cc_start: 0.8594 (tt0) cc_final: 0.8354 (mt0)
REVERT: G   28 ILE cc_start: 0.8074 (mp) cc_final: 0.7859 (mp)
REVERT: R   65 TYR cc_start: 0.8083 (m-80) cc_final: 0.7497 (m-80)
  outliers start: 32
  outliers final: 27
  residues processed: 232
  average time/residue: 0.1180
  time to fit residues: 35.1385
Evaluate side-chains
  241 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  200 PHE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  268 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 377 ASN
N  53 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.147521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.128455 restraints weight = 11994.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.25
r_work: 0.3509 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8470  Z= 0.144
  Angle     :  0.617  13.784  11496  Z= 0.311
  Chirality :  0.043   0.167   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.261 142.021   1161
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.62 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.10 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.27), residues: 1022
  helix:  1.28 (0.27), residues: 394
  sheet: -0.09 (0.37), residues: 215
  loop : -1.17 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.017   0.001   TYR R  32 
 PHE   0.018   0.001   PHE R 199 
 TRP   0.027   0.001   TRP R 170 
 HIS   0.011   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8468)
  covalent geometry    : angle       0.61679 (11492)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.80519 (    4)
  hydrogen bonds       : bond        0.04040 (  384)
  hydrogen bonds       : angle       4.78712 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 210
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8101 (ttpp) cc_final: 0.7792 (ttmm)
REVERT: A  289 GLU cc_start: 0.8004 (tp30) cc_final: 0.7358 (tp30)
REVERT: A  317 GLU cc_start: 0.6965 (mp0) cc_final: 0.6396 (mp0)
REVERT: A  346 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7631 (mtt-85)
REVERT: A  363 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7644 (tpp-160)
REVERT: A  366 PHE cc_start: 0.7948 (t80) cc_final: 0.7495 (t80)
REVERT: A  371 ASP cc_start: 0.8236 (t70) cc_final: 0.7959 (t0)
REVERT: B   49 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7691 (mtt90)
REVERT: B   67 SER cc_start: 0.8816 (m) cc_final: 0.8362 (t)
REVERT: B  103 CYS cc_start: 0.7752 (m) cc_final: 0.7287 (m)
REVERT: B  121 CYS cc_start: 0.8028 (t) cc_final: 0.7651 (t)
REVERT: B  169 TRP cc_start: 0.8622 (m100) cc_final: 0.8160 (m100)
REVERT: B  220 GLN cc_start: 0.7962 (pt0) cc_final: 0.7592 (pt0)
REVERT: B  223 THR cc_start: 0.7755 (m) cc_final: 0.7548 (p)
REVERT: B  256 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7845 (ptp-110)
REVERT: B  258 ASP cc_start: 0.8096 (t70) cc_final: 0.7351 (t0)
REVERT: B  259 GLN cc_start: 0.8582 (tt0) cc_final: 0.8336 (mt0)
REVERT: G   28 ILE cc_start: 0.8034 (mp) cc_final: 0.7820 (mp)
REVERT: R   32 TYR cc_start: 0.7577 (t80) cc_final: 0.7345 (t80)
REVERT: R   65 TYR cc_start: 0.8051 (m-80) cc_final: 0.7528 (m-80)
REVERT: R  272 MET cc_start: 0.7710 (mtt) cc_final: 0.7228 (mmm)
  outliers start: 26
  outliers final: 24
  residues processed: 227
  average time/residue: 0.1178
  time to fit residues: 34.1973
Evaluate side-chains
  236 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  200 PHE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  268 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0670
   chunk 22 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 377 ASN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128133 restraints weight = 12028.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.25
r_work: 0.3505 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8470  Z= 0.161
  Angle     :  0.640  13.666  11496  Z= 0.322
  Chirality :  0.044   0.178   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.205 141.706   1161
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.72 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 23.21 %
    Favored  : 73.77 %
  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: -0.03 (0.27), residues: 1022
  helix:  1.26 (0.27), residues: 393
  sheet: -0.11 (0.37), residues: 215
  loop : -1.19 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.016   0.001   TYR R  32 
 PHE   0.018   0.001   PHE R 199 
 TRP   0.028   0.002   TRP R 170 
 HIS   0.007   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8468)
  covalent geometry    : angle       0.64021 (11492)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       0.84512 (    4)
  hydrogen bonds       : bond        0.04098 (  384)
  hydrogen bonds       : angle       4.80377 ( 1104)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7789 (ttmm)
REVERT: A  289 GLU cc_start: 0.8003 (tp30) cc_final: 0.7355 (tp30)
REVERT: A  309 THR cc_start: 0.8189 (t) cc_final: 0.7901 (p)
REVERT: A  317 GLU cc_start: 0.6940 (mp0) cc_final: 0.6377 (mp0)
REVERT: A  346 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7696 (mtt-85)
REVERT: A  363 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7640 (tpp-160)
REVERT: A  366 PHE cc_start: 0.7886 (t80) cc_final: 0.7455 (t80)
REVERT: A  371 ASP cc_start: 0.8244 (t70) cc_final: 0.7939 (t0)
REVERT: B   49 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7722 (mtt90)
REVERT: B   63 TRP cc_start: 0.8097 (m100) cc_final: 0.7748 (m100)
REVERT: B   67 SER cc_start: 0.8846 (m) cc_final: 0.8407 (t)
REVERT: B  103 CYS cc_start: 0.7784 (m) cc_final: 0.7291 (m)
REVERT: B  121 CYS cc_start: 0.8054 (t) cc_final: 0.7688 (t)
REVERT: B  169 TRP cc_start: 0.8624 (m100) cc_final: 0.8164 (m100)
REVERT: B  220 GLN cc_start: 0.7963 (pt0) cc_final: 0.7553 (pt0)
REVERT: B  223 THR cc_start: 0.7783 (m) cc_final: 0.7574 (p)
REVERT: B  256 ARG cc_start: 0.8234 (ptp-110) cc_final: 0.7915 (ptp-110)
REVERT: B  258 ASP cc_start: 0.8078 (t70) cc_final: 0.7397 (t0)
REVERT: B  259 GLN cc_start: 0.8657 (tt0) cc_final: 0.8418 (mt0)
REVERT: G   28 ILE cc_start: 0.8065 (mp) cc_final: 0.7861 (mp)
REVERT: R   32 TYR cc_start: 0.7587 (t80) cc_final: 0.7374 (t80)
REVERT: R   65 TYR cc_start: 0.8073 (m-80) cc_final: 0.7475 (m-80)
REVERT: R  272 MET cc_start: 0.7714 (mtt) cc_final: 0.7233 (mmm)
  outliers start: 27
  outliers final: 25
  residues processed: 236
  average time/residue: 0.1203
  time to fit residues: 36.2434
Evaluate side-chains
  238 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  200 PHE
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  268 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   chunk 50 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 56 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
A 377 ASN
N  53 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.128647 restraints weight = 12161.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.26
r_work: 0.3513 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8470  Z= 0.144
  Angle     :  0.631  13.235  11496  Z= 0.318
  Chirality :  0.044   0.162   1295
  Planarity :  0.004   0.053   1452
  Dihedral  :  9.107 141.880   1161
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.33 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.10 %
    Favored  : 73.77 %
  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: -0.00 (0.27), residues: 1022
  helix:  1.31 (0.27), residues: 393
  sheet: -0.15 (0.36), residues: 215
  loop : -1.17 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.015   0.001   TYR R  32 
 PHE   0.025   0.001   PHE R  82 
 TRP   0.027   0.001   TRP R 170 
 HIS   0.005   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8468)
  covalent geometry    : angle       0.63058 (11492)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       0.83116 (    4)
  hydrogen bonds       : bond        0.03954 (  384)
  hydrogen bonds       : angle       4.77867 ( 1104)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.52 seconds
wall clock time: 39 minutes 46.02 seconds (2386.02 seconds total)