Starting phenix.real_space_refine
on Fri Aug 22 18:29:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sh7_40480/08_2025/8sh7_40480.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    4283      2.51       5
     N    1164      2.21       5
     O    1318      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6819
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3410
          Classifications: {'peptide': 436}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3348
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' MG': 1, 'GDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.51, per 1000 atoms: 0.22
  Number of scatterers: 6819
  At special positions: 0
  Unit cell: (71.24, 71.24, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       5     15.00
     Mg      1     11.99
     O    1318      8.00
     N    1164      7.00
     C    4283      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.58
  Conformation dependent library (CDL) restraints added in 324.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1590

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      54.4% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
      removed outlier: 3.771A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 4.114A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 79
      removed outlier: 4.811A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 129
      removed outlier: 3.954A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A 124 " --> pdb=" O   ASP A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 3.991A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.525A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   THR A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.571A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 239
      removed outlier: 3.551A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 244
      removed outlier: 3.515A  pdb=" N   ARG A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 258
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.547A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.526A  pdb=" N   CYS A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.591A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.836A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.112A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 436
      removed outlier: 4.080A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 436 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
      removed outlier: 3.623A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.701A  pdb=" N   LEU B  44 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 49
    Processing helix  chain 'B' and resid 70 through 78
      removed outlier: 3.689A  pdb=" N   SER B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 4.366A  pdb=" N   GLN B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 125
      removed outlier: 3.699A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
      removed outlier: 3.907A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.561A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 214
      removed outlier: 3.540A  pdb=" N   ASP B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 3.941A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 3.656A  pdb=" N   GLN B 280 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG B 282 " --> pdb=" O   GLN B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 295
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.871A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.538A  pdb=" N   PHE B 341 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.716A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 4.081A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 424
      removed outlier: 3.521A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.926A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   SER A 140 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL A   9 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 3.613A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92
      removed outlier: 8.357A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   VAL B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   HIS B   6 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   MET B 164 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   TYR B 200 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR B 166 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   SER B 168 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 11.225A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 312 " --> pdb=" O   ASN B 370 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   LYS B 350 " --> pdb=" O   LEU B 311 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL B 313 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   ALA B 352 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA B 315 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   CYS B 354 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   PHE B 317 " --> pdb=" O   CYS B 354 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.539A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    879 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: 0.64

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1435
        1.33 -     1.45: 1626
        1.45 -     1.57: 3829
        1.57 -     1.69: 8
        1.69 -     1.81: 76
  Bond restraints: 6974
  Sorted by residual:
  bond pdb=" N   VAL A  74 "
       pdb=" CA  VAL A  74 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.21e-02 6.83e+03 9.02e+00
  bond pdb=" N   VAL A  68 "
       pdb=" CA  VAL A  68 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 8.91e+00
  bond pdb=" N   CYS B 354 "
       pdb=" CA  CYS B 354 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.035 1.18e-02 7.18e+03 8.58e+00
  bond pdb=" N   VAL B 353 "
       pdb=" CA  VAL B 353 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.57e+00
  bond pdb=" N   ASP A  98 "
       pdb=" CA  ASP A  98 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.037 1.34e-02 5.57e+03 7.50e+00
  ... (remaining 6969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 9207
        2.36 -     4.72: 239
        4.72 -     7.09: 13
        7.09 -     9.45: 7
        9.45 -    11.81: 5
  Bond angle restraints: 9471
  Sorted by residual:
  angle pdb=" CA  GLY B 319 "
        pdb=" C   GLY B 319 "
        pdb=" O   GLY B 319 "
      ideal   model   delta    sigma   weight residual
     121.66  118.05    3.61 8.80e-01 1.29e+00 1.68e+01
  angle pdb=" PA  GTP A 501 "
        pdb=" O3A GTP A 501 "
        pdb=" PB  GTP A 501 "
      ideal   model   delta    sigma   weight residual
     120.50  132.31  -11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C1' GTP A 501 "
        pdb=" C2' GTP A 501 "
        pdb=" C3' GTP A 501 "
      ideal   model   delta    sigma   weight residual
     111.00   99.71   11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" PB  GTP A 501 "
        pdb=" O3B GTP A 501 "
        pdb=" PG  GTP A 501 "
      ideal   model   delta    sigma   weight residual
     120.50  131.68  -11.18 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" N   ALA A  99 "
        pdb=" CA  ALA A  99 "
        pdb=" C   ALA A  99 "
      ideal   model   delta    sigma   weight residual
     112.87  108.73    4.14 1.20e+00 6.94e-01 1.19e+01
  ... (remaining 9466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.73: 4002
       28.73 -    57.46: 117
       57.46 -    86.19: 18
       86.19 -   114.93: 3
      114.93 -   143.66: 3
  Dihedral angle restraints: 4143
    sinusoidal: 1660
      harmonic: 2483
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -39.06  143.66     1      2.00e+01 2.50e-03 4.33e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -157.71 -133.02     1      2.00e+01 2.50e-03 4.04e+01
  dihedral pdb=" O3B GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PB  GTP A 501 "
           pdb=" PA  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  172.67  118.41     1      2.00e+01 2.50e-03 3.54e+01
  ... (remaining 4140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 588
       0.045 -    0.091: 311
       0.091 -    0.136: 105
       0.136 -    0.182: 27
       0.182 -    0.227: 3
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  ILE A  93 "
            pdb=" N   ILE A  93 "
            pdb=" C   ILE A  93 "
            pdb=" CB  ILE A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C3' GTP A 501 "
            pdb=" C2' GTP A 501 "
            pdb=" C4' GTP A 501 "
            pdb=" O3' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.69    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  ARG B 241 "
            pdb=" N   ARG B 241 "
            pdb=" C   ARG B 241 "
            pdb=" CB  ARG B 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 320 "    0.280 9.50e-02 1.11e+02   1.25e-01 9.68e+00
        pdb=" NE  ARG B 320 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 320 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 320 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 215 "   -0.275 9.50e-02 1.11e+02   1.23e-01 9.33e+00
        pdb=" NE  ARG A 215 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 215 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 215 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 215 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 241 "   -0.234 9.50e-02 1.11e+02   1.05e-01 7.60e+00
        pdb=" NE  ARG B 241 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 241 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 241 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 241 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 19
        2.53 -     3.12: 5264
        3.12 -     3.72: 9792
        3.72 -     4.31: 14981
        4.31 -     4.90: 25284
  Nonbonded interactions: 55340
  Sorted by model distance:
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG B 501 "
     model   vdw
     1.939 2.170
  nonbonded pdb=" NZ  LYS B 174 "
            pdb=" OE2 GLU B 205 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NH1 ARG B 282 "
            pdb=" OE2 GLU B 288 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS A 311 "
            pdb=" O   GLY A 436 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" N   GLY B 142 "
            pdb=" O1B GDP B 502 "
     model   vdw
     2.453 3.120
  ... (remaining 55335 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:             13.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:7.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
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      :  0.008   0.061   6974  Z= 0.400
  Angle     :  0.923  11.812   9471  Z= 0.544
  Chirality :  0.060   0.227   1034
  Planarity :  0.010   0.125   1234
  Dihedral  : 14.910 143.657   2553
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.25), residues: 856
  helix: -1.38 (0.22), residues: 365
  sheet:  0.55 (0.41), residues: 145
  loop : -0.77 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG B 156 
 TYR   0.025   0.004   TYR A 319 
 PHE   0.017   0.003   PHE A  53 
 TRP   0.039   0.004   TRP B 101 
 HIS   0.008   0.002   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00815 ( 6974)
  covalent geometry    : angle       0.92343 ( 9471)
  hydrogen bonds       : bond        0.25580 (  308)
  hydrogen bonds       : angle       8.29852 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.8708 (tt0) cc_final: 0.8099 (tp30)
REVERT: A  302 MET cc_start: 0.8632 (mtt) cc_final: 0.7950 (mtt)
REVERT: A  423 GLU cc_start: 0.8354 (tp30) cc_final: 0.7776 (tm-30)
REVERT: B   26 ASP cc_start: 0.8404 (t0) cc_final: 0.8078 (t0)
REVERT: B   31 ASP cc_start: 0.8289 (m-30) cc_final: 0.7603 (m-30)
REVERT: B   37 HIS cc_start: 0.8695 (m-70) cc_final: 0.7585 (m-70)
REVERT: B  114 ASP cc_start: 0.8332 (m-30) cc_final: 0.7783 (m-30)
REVERT: B  122 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8586 (tptt)
REVERT: B  145 SER cc_start: 0.8765 (t) cc_final: 0.8541 (p)
REVERT: B  213 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8701 (ttm170)
REVERT: B  299 MET cc_start: 0.9437 (mmp) cc_final: 0.9033 (mmp)
REVERT: B  324 LYS cc_start: 0.8726 (tttp) cc_final: 0.8345 (tttt)
REVERT: B  388 MET cc_start: 0.8318 (mtp) cc_final: 0.8113 (mtp)
REVERT: B  390 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7524 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.6516
  time to fit residues: 95.3251
Evaluate side-chains
  97 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 139 HIS
A 293 ASN
A 356 ASN
B  43 GLN
B 137 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.093800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.081728 restraints weight = 10016.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.16
r_work: 0.2839 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6974  Z= 0.145
  Angle     :  0.582   7.331   9471  Z= 0.309
  Chirality :  0.044   0.140   1034
  Planarity :  0.005   0.039   1234
  Dihedral  : 10.831 147.435    961
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.64 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.28), residues: 856
  helix:  0.51 (0.27), residues: 375
  sheet:  0.61 (0.42), residues: 146
  loop : -0.41 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 402 
 TYR   0.010   0.001   TYR B 310 
 PHE   0.017   0.001   PHE A 255 
 TRP   0.018   0.002   TRP A  21 
 HIS   0.003   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6974)
  covalent geometry    : angle       0.58184 ( 9471)
  hydrogen bonds       : bond        0.06201 (  308)
  hydrogen bonds       : angle       5.04748 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8822 (m-10) cc_final: 0.8559 (m-10)
REVERT: A   26 LEU cc_start: 0.8966 (tp) cc_final: 0.8738 (mt)
REVERT: A  176 GLN cc_start: 0.8250 (mt0) cc_final: 0.7995 (mm-40)
REVERT: A  254 GLU cc_start: 0.8159 (tt0) cc_final: 0.7604 (tp30)
REVERT: A  302 MET cc_start: 0.8525 (mtt) cc_final: 0.7685 (mtt)
REVERT: A  377 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7772 (tmm)
REVERT: A  423 GLU cc_start: 0.8562 (tp30) cc_final: 0.8360 (mt-10)
REVERT: B   26 ASP cc_start: 0.8770 (t0) cc_final: 0.8498 (t0)
REVERT: B   31 ASP cc_start: 0.8440 (m-30) cc_final: 0.7766 (m-30)
REVERT: B   37 HIS cc_start: 0.8678 (m-70) cc_final: 0.7756 (m-70)
REVERT: B  114 ASP cc_start: 0.8193 (m-30) cc_final: 0.7806 (m-30)
REVERT: B  122 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8669 (tptt)
REVERT: B  157 GLU cc_start: 0.8271 (mp0) cc_final: 0.7957 (mp0)
REVERT: B  299 MET cc_start: 0.9330 (mmp) cc_final: 0.8975 (mmp)
REVERT: B  324 LYS cc_start: 0.8779 (tttp) cc_final: 0.8417 (tttm)
REVERT: B  374 ILE cc_start: 0.9129 (tp) cc_final: 0.8819 (tt)
REVERT: B  388 MET cc_start: 0.8367 (mtp) cc_final: 0.8159 (mtp)
REVERT: B  390 ARG cc_start: 0.8374 (ptm-80) cc_final: 0.7628 (tpt170)
REVERT: B  421 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8119 (mt-10)
  outliers start: 8
  outliers final: 2
  residues processed: 126
  average time/residue: 0.6046
  time to fit residues: 79.1955
Evaluate side-chains
  104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   64 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0670
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
B  48 ASN
B 264 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.094258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.082074 restraints weight = 9940.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.13
r_work: 0.2848 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6974  Z= 0.147
  Angle     :  0.542   6.808   9471  Z= 0.282
  Chirality :  0.043   0.131   1034
  Planarity :  0.004   0.042   1234
  Dihedral  : 10.459 160.603    961
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.87 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.28), residues: 856
  helix:  0.91 (0.27), residues: 379
  sheet:  0.55 (0.42), residues: 149
  loop : -0.56 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 402 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.020   0.001   PHE A 255 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6974)
  covalent geometry    : angle       0.54190 ( 9471)
  hydrogen bonds       : bond        0.05073 (  308)
  hydrogen bonds       : angle       4.51535 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8886 (m-10) cc_final: 0.8594 (m-10)
REVERT: A   26 LEU cc_start: 0.9019 (tp) cc_final: 0.8721 (mt)
REVERT: A  176 GLN cc_start: 0.8247 (mt0) cc_final: 0.8016 (mm-40)
REVERT: A  254 GLU cc_start: 0.8104 (tt0) cc_final: 0.7565 (tp30)
REVERT: A  302 MET cc_start: 0.8228 (mtt) cc_final: 0.7597 (mtt)
REVERT: A  411 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7261 (mt-10)
REVERT: A  434 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8026 (tp30)
REVERT: B   24 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (mm)
REVERT: B   26 ASP cc_start: 0.8800 (t0) cc_final: 0.8581 (t0)
REVERT: B   31 ASP cc_start: 0.8483 (m-30) cc_final: 0.7803 (m-30)
REVERT: B   37 HIS cc_start: 0.8719 (m-70) cc_final: 0.7774 (m-70)
REVERT: B  114 ASP cc_start: 0.8222 (m-30) cc_final: 0.7902 (m-30)
REVERT: B  122 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8649 (tptt)
REVERT: B  157 GLU cc_start: 0.8392 (mp0) cc_final: 0.8093 (mp0)
REVERT: B  203 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8356 (m-30)
REVERT: B  299 MET cc_start: 0.9287 (mmp) cc_final: 0.8956 (mmp)
REVERT: B  324 LYS cc_start: 0.8830 (tttp) cc_final: 0.8427 (tttm)
REVERT: B  388 MET cc_start: 0.8441 (mtp) cc_final: 0.7995 (mtm)
REVERT: B  390 ARG cc_start: 0.8348 (ptm-80) cc_final: 0.7593 (tpt170)
REVERT: B  421 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8125 (mt-10)
  outliers start: 16
  outliers final: 4
  residues processed: 120
  average time/residue: 0.5981
  time to fit residues: 74.7393
Evaluate side-chains
  108 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0000
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4162

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
A 256 GLN
B   6 HIS
B   8 GLN
B 280 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.095244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.083099 restraints weight = 9903.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.14
r_work: 0.2855 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6974  Z= 0.123
  Angle     :  0.514   6.777   9471  Z= 0.264
  Chirality :  0.042   0.135   1034
  Planarity :  0.004   0.042   1234
  Dihedral  : 10.171 164.760    961
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.55 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.28), residues: 856
  helix:  1.11 (0.28), residues: 378
  sheet:  0.76 (0.42), residues: 148
  loop : -0.59 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.007   0.001   TYR B 310 
 PHE   0.018   0.001   PHE A 255 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6974)
  covalent geometry    : angle       0.51431 ( 9471)
  hydrogen bonds       : bond        0.04431 (  308)
  hydrogen bonds       : angle       4.31777 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8877 (m-10) cc_final: 0.8570 (m-10)
REVERT: A  176 GLN cc_start: 0.8224 (mt0) cc_final: 0.8006 (mm-40)
REVERT: A  254 GLU cc_start: 0.7933 (tt0) cc_final: 0.7456 (tp30)
REVERT: A  302 MET cc_start: 0.8222 (mtt) cc_final: 0.7811 (mtt)
REVERT: A  377 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7894 (tmm)
REVERT: A  411 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7187 (mt-10)
REVERT: A  423 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6959 (mt-10)
REVERT: A  434 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7971 (tp30)
REVERT: B   26 ASP cc_start: 0.8845 (t0) cc_final: 0.8623 (t0)
REVERT: B   31 ASP cc_start: 0.8264 (m-30) cc_final: 0.7627 (m-30)
REVERT: B   37 HIS cc_start: 0.8751 (m-70) cc_final: 0.7715 (m-70)
REVERT: B  114 ASP cc_start: 0.8200 (m-30) cc_final: 0.7929 (m-30)
REVERT: B  122 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8639 (tptt)
REVERT: B  157 GLU cc_start: 0.8413 (mp0) cc_final: 0.8090 (mp0)
REVERT: B  197 ASP cc_start: 0.8666 (m-30) cc_final: 0.8399 (m-30)
REVERT: B  203 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8355 (m-30)
REVERT: B  288 GLU cc_start: 0.8101 (pt0) cc_final: 0.7800 (pt0)
REVERT: B  324 LYS cc_start: 0.8710 (tttp) cc_final: 0.8384 (tttm)
REVERT: B  332 ASN cc_start: 0.8769 (t0) cc_final: 0.8500 (t0)
REVERT: B  388 MET cc_start: 0.8434 (mtp) cc_final: 0.7991 (mtm)
REVERT: B  390 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7531 (tpt170)
REVERT: B  421 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8165 (mt-10)
  outliers start: 15
  outliers final: 5
  residues processed: 121
  average time/residue: 0.5866
  time to fit residues: 74.0357
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.092778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.080745 restraints weight = 10014.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.12
r_work: 0.2818 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6974  Z= 0.184
  Angle     :  0.551   7.061   9471  Z= 0.284
  Chirality :  0.044   0.132   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.280 165.942    961
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.05 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.28), residues: 856
  helix:  1.09 (0.28), residues: 376
  sheet:  0.81 (0.42), residues: 148
  loop : -0.70 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 221 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.019   0.002   PHE A 255 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 6974)
  covalent geometry    : angle       0.55108 ( 9471)
  hydrogen bonds       : bond        0.05194 (  308)
  hydrogen bonds       : angle       4.41200 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8918 (m-10) cc_final: 0.8590 (m-10)
REVERT: A  176 GLN cc_start: 0.8130 (mt0) cc_final: 0.7876 (mm-40)
REVERT: A  254 GLU cc_start: 0.8171 (tt0) cc_final: 0.7592 (tp30)
REVERT: A  302 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7847 (mtt)
REVERT: A  377 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7894 (tmm)
REVERT: A  411 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7243 (mt-10)
REVERT: A  423 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7010 (mt-10)
REVERT: A  434 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8008 (tp30)
REVERT: B   26 ASP cc_start: 0.8850 (t0) cc_final: 0.8615 (t0)
REVERT: B   31 ASP cc_start: 0.8242 (m-30) cc_final: 0.7554 (m-30)
REVERT: B   37 HIS cc_start: 0.8768 (m-70) cc_final: 0.7661 (m-70)
REVERT: B  114 ASP cc_start: 0.8277 (m-30) cc_final: 0.7967 (m-30)
REVERT: B  157 GLU cc_start: 0.8345 (mp0) cc_final: 0.8022 (mp0)
REVERT: B  197 ASP cc_start: 0.8744 (m-30) cc_final: 0.8456 (m-30)
REVERT: B  203 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8494 (m-30)
REVERT: B  288 GLU cc_start: 0.8165 (pt0) cc_final: 0.7885 (pt0)
REVERT: B  324 LYS cc_start: 0.8824 (tttp) cc_final: 0.8467 (tttm)
REVERT: B  388 MET cc_start: 0.8443 (mtp) cc_final: 0.8042 (mtm)
REVERT: B  390 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.7447 (tpt170)
REVERT: B  421 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8164 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 0.5969
  time to fit residues: 71.8370
Evaluate side-chains
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   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 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.093195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.081023 restraints weight = 10056.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.15
r_work: 0.2830 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6974  Z= 0.173
  Angle     :  0.546   7.023   9471  Z= 0.281
  Chirality :  0.044   0.138   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.274 167.591    961
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.05 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.28), residues: 856
  helix:  1.08 (0.27), residues: 379
  sheet:  0.90 (0.42), residues: 148
  loop : -0.77 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.020   0.001   PHE A 255 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6974)
  covalent geometry    : angle       0.54645 ( 9471)
  hydrogen bonds       : bond        0.05039 (  308)
  hydrogen bonds       : angle       4.37362 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8910 (m-10) cc_final: 0.8573 (m-10)
REVERT: A  176 GLN cc_start: 0.8239 (mt0) cc_final: 0.8010 (mm-40)
REVERT: A  254 GLU cc_start: 0.8180 (tt0) cc_final: 0.7599 (tp30)
REVERT: A  302 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7861 (mtt)
REVERT: A  377 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7884 (tmm)
REVERT: A  411 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7210 (mt-10)
REVERT: A  423 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7008 (mt-10)
REVERT: A  434 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7994 (tp30)
REVERT: B   26 ASP cc_start: 0.8845 (t0) cc_final: 0.8606 (t0)
REVERT: B   31 ASP cc_start: 0.8246 (m-30) cc_final: 0.7543 (m-30)
REVERT: B   37 HIS cc_start: 0.8786 (m-70) cc_final: 0.7675 (m-70)
REVERT: B  114 ASP cc_start: 0.8259 (m-30) cc_final: 0.7914 (m-30)
REVERT: B  157 GLU cc_start: 0.8401 (mp0) cc_final: 0.8024 (mp0)
REVERT: B  197 ASP cc_start: 0.8764 (m-30) cc_final: 0.8478 (m-30)
REVERT: B  203 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8512 (m-30)
REVERT: B  288 GLU cc_start: 0.8138 (pt0) cc_final: 0.7867 (pt0)
REVERT: B  324 LYS cc_start: 0.8813 (tttp) cc_final: 0.8462 (tttm)
REVERT: B  388 MET cc_start: 0.8453 (mtp) cc_final: 0.8042 (mtm)
REVERT: B  390 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.7434 (tpt170)
REVERT: B  421 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8161 (mt-10)
  outliers start: 16
  outliers final: 5
  residues processed: 116
  average time/residue: 0.6092
  time to fit residues: 73.9165
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0770
   chunk 65 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.094501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.082337 restraints weight = 9898.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.13
r_work: 0.2844 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6974  Z= 0.132
  Angle     :  0.515   6.716   9471  Z= 0.263
  Chirality :  0.042   0.134   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.144 168.927    961
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.87 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.28), residues: 856
  helix:  1.15 (0.27), residues: 381
  sheet:  1.03 (0.42), residues: 148
  loop : -0.69 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 221 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.002   0.001   HIS A  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6974)
  covalent geometry    : angle       0.51456 ( 9471)
  hydrogen bonds       : bond        0.04445 (  308)
  hydrogen bonds       : angle       4.23690 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8897 (m-10) cc_final: 0.8600 (m-10)
REVERT: A  176 GLN cc_start: 0.8242 (mt0) cc_final: 0.8016 (mm-40)
REVERT: A  254 GLU cc_start: 0.7984 (tt0) cc_final: 0.7473 (tp30)
REVERT: A  302 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7850 (mtt)
REVERT: A  377 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7850 (tmm)
REVERT: A  411 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7373 (mt-10)
REVERT: A  414 GLU cc_start: 0.8761 (pt0) cc_final: 0.8164 (pm20)
REVERT: A  423 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6996 (mt-10)
REVERT: A  434 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7973 (tp30)
REVERT: B   26 ASP cc_start: 0.8841 (t0) cc_final: 0.8594 (t0)
REVERT: B   31 ASP cc_start: 0.8252 (m-30) cc_final: 0.7495 (m-30)
REVERT: B   37 HIS cc_start: 0.8796 (m-70) cc_final: 0.7921 (m170)
REVERT: B  114 ASP cc_start: 0.8228 (m-30) cc_final: 0.7890 (m-30)
REVERT: B  157 GLU cc_start: 0.8341 (mp0) cc_final: 0.8062 (mp0)
REVERT: B  197 ASP cc_start: 0.8726 (m-30) cc_final: 0.8462 (m-30)
REVERT: B  203 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8473 (m-30)
REVERT: B  324 LYS cc_start: 0.8714 (tttp) cc_final: 0.8378 (tttm)
REVERT: B  388 MET cc_start: 0.8428 (mtp) cc_final: 0.8026 (mtm)
REVERT: B  390 ARG cc_start: 0.8333 (ptm-80) cc_final: 0.7517 (tpt170)
REVERT: B  421 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8171 (mt-10)
  outliers start: 12
  outliers final: 4
  residues processed: 115
  average time/residue: 0.6341
  time to fit residues: 76.2061
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 70 optimal weight:    0.0570
   chunk 37 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0070
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 56 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.3516

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.095817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.083683 restraints weight = 9916.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.13
r_work: 0.2874 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6974  Z= 0.112
  Angle     :  0.500   6.523   9471  Z= 0.254
  Chirality :  0.042   0.135   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.038 169.411    961
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.14 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.29), residues: 856
  helix:  1.27 (0.28), residues: 377
  sheet:  1.11 (0.42), residues: 148
  loop : -0.54 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 422 
 TYR   0.006   0.001   TYR B 310 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.015   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6974)
  covalent geometry    : angle       0.49959 ( 9471)
  hydrogen bonds       : bond        0.04042 (  308)
  hydrogen bonds       : angle       4.12375 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8920 (m-10) cc_final: 0.8621 (m-10)
REVERT: A  176 GLN cc_start: 0.8107 (mt0) cc_final: 0.7865 (mm-40)
REVERT: A  254 GLU cc_start: 0.7909 (tt0) cc_final: 0.7454 (mm-30)
REVERT: A  302 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7767 (mtt)
REVERT: A  411 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7409 (mt-10)
REVERT: A  414 GLU cc_start: 0.8710 (pt0) cc_final: 0.8133 (pm20)
REVERT: A  423 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7012 (mt-10)
REVERT: A  434 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7929 (tp30)
REVERT: B   26 ASP cc_start: 0.8843 (t0) cc_final: 0.8588 (t0)
REVERT: B   31 ASP cc_start: 0.8270 (m-30) cc_final: 0.7515 (m-30)
REVERT: B   37 HIS cc_start: 0.8771 (m-70) cc_final: 0.7858 (m170)
REVERT: B   41 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8363 (p0)
REVERT: B  114 ASP cc_start: 0.8212 (m-30) cc_final: 0.7893 (m-30)
REVERT: B  157 GLU cc_start: 0.8319 (mp0) cc_final: 0.8051 (mp0)
REVERT: B  197 ASP cc_start: 0.8683 (m-30) cc_final: 0.8436 (m-30)
REVERT: B  203 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (m-30)
REVERT: B  324 LYS cc_start: 0.8793 (tttp) cc_final: 0.8471 (tttm)
REVERT: B  332 ASN cc_start: 0.8759 (t0) cc_final: 0.8498 (t0)
REVERT: B  388 MET cc_start: 0.8398 (mtp) cc_final: 0.8010 (mtm)
REVERT: B  390 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7556 (tpt170)
REVERT: B  421 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8179 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 119
  average time/residue: 0.6432
  time to fit residues: 79.9901
Evaluate side-chains
  116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0020
   chunk 41 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.094874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.082777 restraints weight = 9982.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.13
r_work: 0.2860 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6974  Z= 0.132
  Angle     :  0.510   6.620   9471  Z= 0.261
  Chirality :  0.042   0.132   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.083 169.336    961
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.42 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.28), residues: 856
  helix:  1.26 (0.28), residues: 377
  sheet:  1.07 (0.42), residues: 148
  loop : -0.53 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 422 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6974)
  covalent geometry    : angle       0.51032 ( 9471)
  hydrogen bonds       : bond        0.04359 (  308)
  hydrogen bonds       : angle       4.16060 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8899 (m-10) cc_final: 0.8603 (m-10)
REVERT: A  176 GLN cc_start: 0.8128 (mt0) cc_final: 0.7876 (mm-40)
REVERT: A  254 GLU cc_start: 0.7931 (tt0) cc_final: 0.7491 (mm-30)
REVERT: A  276 ILE cc_start: 0.8852 (pt) cc_final: 0.8633 (tt)
REVERT: A  302 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7835 (mtt)
REVERT: A  411 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7431 (mt-10)
REVERT: A  414 GLU cc_start: 0.8731 (pt0) cc_final: 0.8134 (pm20)
REVERT: A  423 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7013 (mt-10)
REVERT: A  434 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7909 (tp30)
REVERT: B   26 ASP cc_start: 0.8848 (t0) cc_final: 0.8596 (t0)
REVERT: B   31 ASP cc_start: 0.8266 (m-30) cc_final: 0.7504 (m-30)
REVERT: B   37 HIS cc_start: 0.8768 (m-70) cc_final: 0.7841 (m170)
REVERT: B   41 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (p0)
REVERT: B  114 ASP cc_start: 0.8210 (m-30) cc_final: 0.7934 (m-30)
REVERT: B  157 GLU cc_start: 0.8329 (mp0) cc_final: 0.8112 (mp0)
REVERT: B  197 ASP cc_start: 0.8701 (m-30) cc_final: 0.8446 (m-30)
REVERT: B  324 LYS cc_start: 0.8821 (tttp) cc_final: 0.8490 (tttm)
REVERT: B  388 MET cc_start: 0.8394 (mtp) cc_final: 0.7983 (mtm)
REVERT: B  390 ARG cc_start: 0.8292 (ptm-80) cc_final: 0.7500 (tpt170)
REVERT: B  421 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8183 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 112
  average time/residue: 0.6423
  time to fit residues: 75.0950
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
A 309 HIS
B   6 HIS
B   8 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.094116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.082029 restraints weight = 9910.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.12
r_work: 0.2848 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6974  Z= 0.150
  Angle     :  0.528   6.733   9471  Z= 0.270
  Chirality :  0.043   0.132   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.165 169.452    961
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.28 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.28), residues: 856
  helix:  1.23 (0.27), residues: 381
  sheet:  1.08 (0.42), residues: 148
  loop : -0.66 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 422 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.020   0.001   PHE A 255 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6974)
  covalent geometry    : angle       0.52822 ( 9471)
  hydrogen bonds       : bond        0.04598 (  308)
  hydrogen bonds       : angle       4.21552 (  879)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8908 (m-10) cc_final: 0.8613 (m-10)
REVERT: A  176 GLN cc_start: 0.8141 (mt0) cc_final: 0.7886 (mm-40)
REVERT: A  254 GLU cc_start: 0.7945 (tt0) cc_final: 0.7497 (mm-30)
REVERT: A  302 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7869 (mtt)
REVERT: A  377 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7893 (tmm)
REVERT: A  411 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7426 (mt-10)
REVERT: A  414 GLU cc_start: 0.8726 (pt0) cc_final: 0.8148 (pm20)
REVERT: A  423 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7004 (mt-10)
REVERT: A  434 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7909 (tp30)
REVERT: B   26 ASP cc_start: 0.8842 (t0) cc_final: 0.8593 (t0)
REVERT: B   31 ASP cc_start: 0.8262 (m-30) cc_final: 0.7494 (m-30)
REVERT: B   37 HIS cc_start: 0.8746 (m-70) cc_final: 0.7795 (m170)
REVERT: B   41 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (p0)
REVERT: B  114 ASP cc_start: 0.8168 (m-30) cc_final: 0.7918 (m-30)
REVERT: B  147 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8408 (tpp)
REVERT: B  157 GLU cc_start: 0.8373 (mp0) cc_final: 0.8130 (mp0)
REVERT: B  197 ASP cc_start: 0.8720 (m-30) cc_final: 0.8449 (m-30)
REVERT: B  324 LYS cc_start: 0.8833 (tttp) cc_final: 0.8488 (tttm)
REVERT: B  388 MET cc_start: 0.8424 (mtp) cc_final: 0.8008 (mtm)
REVERT: B  390 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7500 (tpt170)
REVERT: B  421 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8185 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 113
  average time/residue: 0.6674
  time to fit residues: 78.4406
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 36 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
A 309 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.093384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.081259 restraints weight = 9917.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.12
r_work: 0.2830 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6974  Z= 0.166
  Angle     :  0.545   6.849   9471  Z= 0.279
  Chirality :  0.043   0.132   1034
  Planarity :  0.004   0.040   1234
  Dihedral  : 10.237 169.376    961
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.28 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.28), residues: 856
  helix:  1.17 (0.27), residues: 381
  sheet:  1.04 (0.42), residues: 148
  loop : -0.71 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 422 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.021   0.001   PHE A 255 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6974)
  covalent geometry    : angle       0.54467 ( 9471)
  hydrogen bonds       : bond        0.04818 (  308)
  hydrogen bonds       : angle       4.27529 (  879)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2296.71 seconds
wall clock time: 40 minutes 4.77 seconds (2404.77 seconds total)