Starting phenix.real_space_refine
on Tue Feb 11 23:54:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sh7_40480/02_2025/8sh7_40480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sh7_40480/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sh7_40480/02_2025/8sh7_40480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sh7_40480/02_2025/8sh7_40480.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sh7_40480/02_2025/8sh7_40480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sh7_40480/02_2025/8sh7_40480.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.88, per 1000 atoms: 1.01
  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: 1.96
  Conformation dependent library (CDL) restraints added in 902.8 milliseconds
  

  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: 0.72
  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: 2.01

  Time building geometry restraints manager: 1.93 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:             6.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.460
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.020
-------------------------------------------------------------------------------
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= 0.530
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.039   0.004   TRP B 101 
 HIS   0.008   0.002   HIS A   8 
 PHE   0.017   0.003   PHE A  53 
 TYR   0.025   0.004   TYR A 319 
 ARG   0.021   0.003   ARG B 156 

*********************** 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  : 0.807 
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: 1.6509
  time to fit residues: 241.7340
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  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 139 HIS
A 293 ASN
A 356 ASN
A 406 HIS
B  43 GLN
B 137 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.092277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.080267 restraints weight = 9958.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.13
r_work: 0.2815 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6974  Z= 0.292
  Angle     :  0.623   7.728   9471  Z= 0.331
  Chirality :  0.046   0.159   1034
  Planarity :  0.005   0.039   1234
  Dihedral  : 11.076 151.903    961
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.37 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.27), residues: 856
  helix:  0.41 (0.26), residues: 381
  sheet:  0.62 (0.42), residues: 145
  loop : -0.65 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  21 
 HIS   0.004   0.001   HIS B  28 
 PHE   0.018   0.002   PHE A 255 
 TYR   0.011   0.001   TYR A 103 
 ARG   0.005   0.001   ARG A 402 

*********************** 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: 11
    poor density    : 118
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8829 (m-10) cc_final: 0.8565 (m-10)
REVERT: A   26 LEU cc_start: 0.8992 (tp) cc_final: 0.8739 (mt)
REVERT: A  176 GLN cc_start: 0.8292 (mt0) cc_final: 0.8054 (mm-40)
REVERT: A  254 GLU cc_start: 0.8228 (tt0) cc_final: 0.7588 (tp30)
REVERT: A  290 GLU cc_start: 0.8865 (tt0) cc_final: 0.8634 (mt-10)
REVERT: A  302 MET cc_start: 0.8609 (mtt) cc_final: 0.7880 (mtt)
REVERT: A  377 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7844 (tmm)
REVERT: A  393 HIS cc_start: 0.9059 (t70) cc_final: 0.8846 (t70)
REVERT: A  423 GLU cc_start: 0.8579 (tp30) cc_final: 0.8354 (mt-10)
REVERT: B   26 ASP cc_start: 0.8791 (t0) cc_final: 0.8522 (t0)
REVERT: B   31 ASP cc_start: 0.8445 (m-30) cc_final: 0.7763 (m-30)
REVERT: B   37 HIS cc_start: 0.8700 (m-70) cc_final: 0.7794 (m-70)
REVERT: B  114 ASP cc_start: 0.8221 (m-30) cc_final: 0.7831 (m-30)
REVERT: B  122 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8657 (tptt)
REVERT: B  157 GLU cc_start: 0.8318 (mp0) cc_final: 0.8048 (mp0)
REVERT: B  299 MET cc_start: 0.9322 (mmp) cc_final: 0.8984 (mmp)
REVERT: B  324 LYS cc_start: 0.8817 (tttp) cc_final: 0.8409 (tttm)
REVERT: B  374 ILE cc_start: 0.9123 (tp) cc_final: 0.8879 (tt)
REVERT: B  390 ARG cc_start: 0.8372 (ptm-80) cc_final: 0.7509 (tpt170)
REVERT: B  421 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8122 (mt-10)
  outliers start: 11
  outliers final: 2
  residues processed: 122
  average time/residue: 1.5550
  time to fit residues: 197.6320
Evaluate side-chains
  100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0060
   chunk 52 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
B   6 HIS
B   8 GLN
B 264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.093970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.081727 restraints weight = 10007.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.16
r_work: 0.2834 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6974  Z= 0.221
  Angle     :  0.542   6.796   9471  Z= 0.283
  Chirality :  0.043   0.132   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.463 159.156    961
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 11.60 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.28), residues: 856
  helix:  0.87 (0.27), residues: 378
  sheet:  0.61 (0.42), residues: 148
  loop : -0.69 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  21 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.009   0.001   TYR B 310 
 ARG   0.004   0.000   ARG A 402 

*********************** 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
  129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8873 (m-10) cc_final: 0.8569 (m-10)
REVERT: A   26 LEU cc_start: 0.9016 (tp) cc_final: 0.8718 (mt)
REVERT: A  176 GLN cc_start: 0.8248 (mt0) cc_final: 0.8019 (mm-40)
REVERT: A  254 GLU cc_start: 0.8183 (tt0) cc_final: 0.7589 (tp30)
REVERT: A  302 MET cc_start: 0.8298 (mtt) cc_final: 0.7788 (mtt)
REVERT: A  434 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8037 (tp30)
REVERT: B   26 ASP cc_start: 0.8813 (t0) cc_final: 0.8589 (t0)
REVERT: B   31 ASP cc_start: 0.8484 (m-30) cc_final: 0.7781 (m-30)
REVERT: B   37 HIS cc_start: 0.8716 (m-70) cc_final: 0.7705 (m-70)
REVERT: B  114 ASP cc_start: 0.8248 (m-30) cc_final: 0.7921 (m-30)
REVERT: B  122 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8640 (tptt)
REVERT: B  157 GLU cc_start: 0.8360 (mp0) cc_final: 0.8145 (mp0)
REVERT: B  203 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8367 (m-30)
REVERT: B  299 MET cc_start: 0.9286 (mmp) cc_final: 0.8949 (mmp)
REVERT: B  324 LYS cc_start: 0.8840 (tttp) cc_final: 0.8439 (tttm)
REVERT: B  388 MET cc_start: 0.8291 (mtp) cc_final: 0.7896 (mtm)
REVERT: B  390 ARG cc_start: 0.8348 (ptm-80) cc_final: 0.7528 (tpt170)
REVERT: B  421 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8134 (mt-10)
  outliers start: 17
  outliers final: 5
  residues processed: 121
  average time/residue: 1.6471
  time to fit residues: 207.3673
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  : 0.776 
-------------------------------------------------------------------------------
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  435 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 11 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0060
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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  48 ASN
B 280 GLN

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 = 0.093980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.081808 restraints weight = 9964.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.13
r_work: 0.2836 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6974  Z= 0.219
  Angle     :  0.531   7.209   9471  Z= 0.273
  Chirality :  0.043   0.134   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.238 163.601    961
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.28), residues: 856
  helix:  1.05 (0.28), residues: 378
  sheet:  0.69 (0.42), residues: 148
  loop : -0.68 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  21 
 HIS   0.004   0.001   HIS B 264 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.009   0.001   TYR A 103 
 ARG   0.004   0.000   ARG A 221 

*********************** 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
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8887 (m-10) cc_final: 0.8582 (m-10)
REVERT: A  176 GLN cc_start: 0.8236 (mt0) cc_final: 0.8002 (mm-40)
REVERT: A  254 GLU cc_start: 0.8114 (tt0) cc_final: 0.7588 (tp30)
REVERT: A  302 MET cc_start: 0.8270 (mtt) cc_final: 0.7840 (mtt)
REVERT: A  377 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7889 (tmm)
REVERT: A  423 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6987 (mt-10)
REVERT: A  434 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8054 (tp30)
REVERT: B   26 ASP cc_start: 0.8837 (t0) cc_final: 0.8616 (t0)
REVERT: B   31 ASP cc_start: 0.8266 (m-30) cc_final: 0.7630 (m-30)
REVERT: B   37 HIS cc_start: 0.8752 (m-70) cc_final: 0.7733 (m-70)
REVERT: B  114 ASP cc_start: 0.8206 (m-30) cc_final: 0.7932 (m-30)
REVERT: B  122 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8651 (tptt)
REVERT: B  157 GLU cc_start: 0.8353 (mp0) cc_final: 0.8094 (mp0)
REVERT: B  197 ASP cc_start: 0.8704 (m-30) cc_final: 0.8429 (m-30)
REVERT: B  203 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8430 (m-30)
REVERT: B  288 GLU cc_start: 0.8107 (pt0) cc_final: 0.7819 (pt0)
REVERT: B  324 LYS cc_start: 0.8744 (tttp) cc_final: 0.8398 (tttm)
REVERT: B  388 MET cc_start: 0.8305 (mtp) cc_final: 0.7935 (mtm)
REVERT: B  390 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.7495 (tpt170)
REVERT: B  421 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8185 (mt-10)
  outliers start: 17
  outliers final: 4
  residues processed: 123
  average time/residue: 1.5337
  time to fit residues: 197.1177
Evaluate side-chains
  107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0170
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3143 r_free = 0.3143 target = 0.094277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.082180 restraints weight = 9942.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.13
r_work: 0.2846 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6974  Z= 0.205
  Angle     :  0.519   6.767   9471  Z= 0.266
  Chirality :  0.042   0.134   1034
  Planarity :  0.004   0.041   1234
  Dihedral  : 10.142 166.166    961
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.19 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 856
  helix:  1.11 (0.28), residues: 379
  sheet:  0.88 (0.42), residues: 148
  loop : -0.69 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.008   0.001   TYR A 103 
 ARG   0.003   0.000   ARG A 221 

*********************** 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: 14
    poor density    : 107
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8902 (m-10) cc_final: 0.8585 (m-10)
REVERT: A  176 GLN cc_start: 0.8225 (mt0) cc_final: 0.8002 (mm-40)
REVERT: A  254 GLU cc_start: 0.8107 (tt0) cc_final: 0.7570 (tp30)
REVERT: A  302 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7804 (mtt)
REVERT: A  377 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7874 (tmm)
REVERT: A  423 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7005 (mt-10)
REVERT: A  434 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7936 (tp30)
REVERT: A  437 VAL cc_start: 0.8339 (t) cc_final: 0.8074 (p)
REVERT: B   26 ASP cc_start: 0.8857 (t0) cc_final: 0.8621 (t0)
REVERT: B   31 ASP cc_start: 0.8261 (m-30) cc_final: 0.7591 (m-30)
REVERT: B   37 HIS cc_start: 0.8763 (m-70) cc_final: 0.7677 (m-70)
REVERT: B  114 ASP cc_start: 0.8189 (m-30) cc_final: 0.7903 (m-30)
REVERT: B  157 GLU cc_start: 0.8358 (mp0) cc_final: 0.8038 (mp0)
REVERT: B  197 ASP cc_start: 0.8709 (m-30) cc_final: 0.8442 (m-30)
REVERT: B  203 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (m-30)
REVERT: B  288 GLU cc_start: 0.8117 (pt0) cc_final: 0.7831 (pt0)
REVERT: B  324 LYS cc_start: 0.8727 (tttp) cc_final: 0.8396 (tttm)
REVERT: B  388 MET cc_start: 0.8306 (mtp) cc_final: 0.7904 (mtm)
REVERT: B  390 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.7458 (tpt170)
REVERT: B  421 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8162 (mt-10)
  outliers start: 14
  outliers final: 6
  residues processed: 114
  average time/residue: 1.5675
  time to fit residues: 186.2454
Evaluate side-chains
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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  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
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 29 optimal weight:    0.0870
   chunk 74 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0470
   chunk 77 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0000
   overall best weight:    0.2460

-------------------------------------------------------------------------------
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 = 0.3180 r_free = 0.3180 target = 0.096869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.084728 restraints weight = 9913.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.14
r_work: 0.2885 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6974  Z= 0.142
  Angle     :  0.485   6.419   9471  Z= 0.245
  Chirality :  0.041   0.137   1034
  Planarity :  0.004   0.039   1234
  Dihedral  :  9.933 167.552    961
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.14 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.29), residues: 856
  helix:  1.35 (0.28), residues: 372
  sheet:  0.99 (0.42), residues: 149
  loop : -0.50 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  21 
 HIS   0.001   0.000   HIS A   8 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.006   0.001   TYR B 310 
 ARG   0.003   0.000   ARG A 402 

*********************** 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
  122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8908 (m-10) cc_final: 0.8598 (m-10)
REVERT: A  176 GLN cc_start: 0.8114 (mt0) cc_final: 0.7879 (mm-40)
REVERT: A  254 GLU cc_start: 0.7868 (tt0) cc_final: 0.7411 (tp30)
REVERT: A  302 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7760 (mtt)
REVERT: A  414 GLU cc_start: 0.8707 (pt0) cc_final: 0.8152 (pm20)
REVERT: A  423 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7065 (mt-10)
REVERT: A  434 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7991 (tp30)
REVERT: A  437 VAL cc_start: 0.8223 (t) cc_final: 0.7794 (p)
REVERT: B   26 ASP cc_start: 0.8872 (t0) cc_final: 0.8624 (t0)
REVERT: B   31 ASP cc_start: 0.8285 (m-30) cc_final: 0.7567 (m-30)
REVERT: B   37 HIS cc_start: 0.8764 (m-70) cc_final: 0.7989 (m170)
REVERT: B  114 ASP cc_start: 0.8241 (m-30) cc_final: 0.7876 (m-30)
REVERT: B  157 GLU cc_start: 0.8373 (mp0) cc_final: 0.8104 (mp0)
REVERT: B  197 ASP cc_start: 0.8657 (m-30) cc_final: 0.8430 (m-30)
REVERT: B  203 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8298 (m-30)
REVERT: B  324 LYS cc_start: 0.8715 (tttp) cc_final: 0.8409 (tttm)
REVERT: B  332 ASN cc_start: 0.8706 (t0) cc_final: 0.8450 (t0)
REVERT: B  388 MET cc_start: 0.8247 (mtp) cc_final: 0.7833 (mtm)
REVERT: B  390 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7574 (tpt170)
REVERT: B  421 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8123 (mt-10)
  outliers start: 9
  outliers final: 3
  residues processed: 117
  average time/residue: 1.5038
  time to fit residues: 183.8089
Evaluate side-chains
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue   64 VAL
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 47 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0470
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3143 r_free = 0.3143 target = 0.094296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.082223 restraints weight = 9918.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.13
r_work: 0.2847 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2959

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= 0.229
  Angle     :  0.523   6.747   9471  Z= 0.267
  Chirality :  0.043   0.132   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.074 168.076    961
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.28), residues: 856
  helix:  1.26 (0.28), residues: 373
  sheet:  1.06 (0.42), residues: 148
  loop : -0.54 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  28 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.009   0.001   TYR A 103 
 ARG   0.003   0.000   ARG A 422 

*********************** 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  : 0.737 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8901 (m-10) cc_final: 0.8606 (m-10)
REVERT: A  176 GLN cc_start: 0.8127 (mt0) cc_final: 0.7882 (mm-40)
REVERT: A  254 GLU cc_start: 0.7923 (tt0) cc_final: 0.7440 (tp30)
REVERT: A  302 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7856 (mtt)
REVERT: A  390 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7984 (mtm-85)
REVERT: A  414 GLU cc_start: 0.8740 (pt0) cc_final: 0.8163 (pm20)
REVERT: A  423 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7015 (mt-10)
REVERT: A  434 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7927 (tp30)
REVERT: A  437 VAL cc_start: 0.8366 (t) cc_final: 0.8118 (p)
REVERT: B   26 ASP cc_start: 0.8863 (t0) cc_final: 0.8619 (t0)
REVERT: B   31 ASP cc_start: 0.8255 (m-30) cc_final: 0.7511 (m-30)
REVERT: B   37 HIS cc_start: 0.8779 (m-70) cc_final: 0.7960 (m170)
REVERT: B  114 ASP cc_start: 0.8222 (m-30) cc_final: 0.7892 (m-30)
REVERT: B  147 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8148 (tpp)
REVERT: B  157 GLU cc_start: 0.8341 (mp0) cc_final: 0.8069 (mp0)
REVERT: B  197 ASP cc_start: 0.8701 (m-30) cc_final: 0.8439 (m-30)
REVERT: B  203 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8459 (m-30)
REVERT: B  324 LYS cc_start: 0.8843 (tttp) cc_final: 0.8507 (tttm)
REVERT: B  388 MET cc_start: 0.8310 (mtp) cc_final: 0.7835 (mtm)
REVERT: B  390 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.7515 (tpt170)
REVERT: B  421 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8179 (mt-10)
  outliers start: 12
  outliers final: 5
  residues processed: 117
  average time/residue: 1.5771
  time to fit residues: 192.3673
Evaluate side-chains
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  257 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 78 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0670
   overall best weight:    0.6320

-------------------------------------------------------------------------------
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 = 0.3132 r_free = 0.3132 target = 0.093622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.081574 restraints weight = 9931.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.12
r_work: 0.2834 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6974  Z= 0.248
  Angle     :  0.538   6.847   9471  Z= 0.276
  Chirality :  0.043   0.132   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.186 169.403    961
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.28 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 856
  helix:  1.18 (0.28), residues: 379
  sheet:  1.02 (0.41), residues: 148
  loop : -0.71 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.020   0.001   PHE A 255 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.003   0.000   ARG A 422 

*********************** 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
  120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8905 (m-10) cc_final: 0.8580 (m-10)
REVERT: A  176 GLN cc_start: 0.8150 (mt0) cc_final: 0.7898 (mm-40)
REVERT: A  254 GLU cc_start: 0.7968 (tt0) cc_final: 0.7490 (tp30)
REVERT: A  302 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7897 (mtt)
REVERT: A  423 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7020 (mt-10)
REVERT: A  434 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7902 (tp30)
REVERT: A  437 VAL cc_start: 0.8459 (t) cc_final: 0.7981 (p)
REVERT: B   26 ASP cc_start: 0.8855 (t0) cc_final: 0.8612 (t0)
REVERT: B   31 ASP cc_start: 0.8268 (m-30) cc_final: 0.7496 (m-30)
REVERT: B   37 HIS cc_start: 0.8782 (m-70) cc_final: 0.7875 (m170)
REVERT: B  114 ASP cc_start: 0.8232 (m-30) cc_final: 0.7924 (m-30)
REVERT: B  147 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8214 (tpp)
REVERT: B  197 ASP cc_start: 0.8759 (m-30) cc_final: 0.8476 (m-30)
REVERT: B  203 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8496 (m-30)
REVERT: B  324 LYS cc_start: 0.8787 (tttp) cc_final: 0.8443 (tttm)
REVERT: B  388 MET cc_start: 0.8334 (mtp) cc_final: 0.7859 (mtm)
REVERT: B  390 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7530 (tpt170)
REVERT: B  421 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8186 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 114
  average time/residue: 1.5816
  time to fit residues: 187.9781
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  : 0.760 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  257 MET
Chi-restraints excluded: chain B residue  280 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.1980
   chunk 55 optimal weight:    0.0040
   chunk 29 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.3392

-------------------------------------------------------------------------------
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 = 0.3166 r_free = 0.3166 target = 0.095776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.083732 restraints weight = 9948.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.12
r_work: 0.2872 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6974  Z= 0.168
  Angle     :  0.505   6.500   9471  Z= 0.258
  Chirality :  0.042   0.136   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.053 169.546    961
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.37 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 856
  helix:  1.34 (0.28), residues: 373
  sheet:  1.02 (0.42), residues: 149
  loop : -0.58 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 192 
 PHE   0.019   0.001   PHE A 255 
 TYR   0.006   0.001   TYR A 103 
 ARG   0.003   0.000   ARG A 422 

*********************** 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
  114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8916 (m-10) cc_final: 0.8621 (m-10)
REVERT: A  176 GLN cc_start: 0.8137 (mt0) cc_final: 0.7902 (mm-40)
REVERT: A  254 GLU cc_start: 0.7879 (tt0) cc_final: 0.7414 (tp30)
REVERT: A  302 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7799 (mtt)
REVERT: A  390 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7910 (mtm-85)
REVERT: A  414 GLU cc_start: 0.8711 (pt0) cc_final: 0.8196 (pm20)
REVERT: A  423 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7091 (mt-10)
REVERT: A  434 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7839 (tp30)
REVERT: A  437 VAL cc_start: 0.8377 (t) cc_final: 0.7908 (p)
REVERT: B   26 ASP cc_start: 0.8848 (t0) cc_final: 0.8600 (t0)
REVERT: B   31 ASP cc_start: 0.8271 (m-30) cc_final: 0.7511 (m-30)
REVERT: B   37 HIS cc_start: 0.8750 (m-70) cc_final: 0.7820 (m170)
REVERT: B  114 ASP cc_start: 0.8188 (m-30) cc_final: 0.7914 (m-30)
REVERT: B  147 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (tpp)
REVERT: B  197 ASP cc_start: 0.8689 (m-30) cc_final: 0.8420 (m-30)
REVERT: B  203 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8431 (m-30)
REVERT: B  324 LYS cc_start: 0.8787 (tttp) cc_final: 0.8469 (tttm)
REVERT: B  388 MET cc_start: 0.8299 (mtp) cc_final: 0.7873 (mtm)
REVERT: B  390 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7541 (tpt170)
REVERT: B  421 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8174 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 111
  average time/residue: 1.5806
  time to fit residues: 183.0051
Evaluate side-chains
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  363 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 77 optimal weight:    0.4980
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.093535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.081488 restraints weight = 10132.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.14
r_work: 0.2836 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3000

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= 0.267
  Angle     :  0.552   6.828   9471  Z= 0.283
  Chirality :  0.044   0.131   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.216 169.422    961
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.37 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 856
  helix:  1.20 (0.28), residues: 379
  sheet:  1.05 (0.41), residues: 148
  loop : -0.75 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.021   0.001   PHE A 255 
 TYR   0.010   0.001   TYR A 103 
 ARG   0.004   0.000   ARG B 156 

********************** 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
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   24 TYR cc_start: 0.8904 (m-10) cc_final: 0.8579 (m-10)
REVERT: A  176 GLN cc_start: 0.8164 (mt0) cc_final: 0.7910 (mm-40)
REVERT: A  254 GLU cc_start: 0.7971 (tt0) cc_final: 0.7472 (tp30)
REVERT: A  302 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7933 (mtt)
REVERT: A  414 GLU cc_start: 0.8667 (pt0) cc_final: 0.8160 (pm20)
REVERT: A  423 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7076 (mt-10)
REVERT: A  434 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7857 (tp30)
REVERT: A  437 VAL cc_start: 0.8385 (t) cc_final: 0.7896 (p)
REVERT: B   26 ASP cc_start: 0.8845 (t0) cc_final: 0.8600 (t0)
REVERT: B   37 HIS cc_start: 0.8767 (m-70) cc_final: 0.8526 (m170)
REVERT: B  114 ASP cc_start: 0.8170 (m-30) cc_final: 0.7922 (m-30)
REVERT: B  147 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8346 (tpp)
REVERT: B  197 ASP cc_start: 0.8764 (m-30) cc_final: 0.8473 (m-30)
REVERT: B  324 LYS cc_start: 0.8865 (tttp) cc_final: 0.8512 (tttm)
REVERT: B  362 LYS cc_start: 0.7713 (tppt) cc_final: 0.7344 (tppt)
REVERT: B  388 MET cc_start: 0.8325 (mtp) cc_final: 0.7850 (mtm)
REVERT: B  390 ARG cc_start: 0.8300 (ptm-80) cc_final: 0.7517 (tpt170)
REVERT: B  421 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8177 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 110
  average time/residue: 1.5256
  time to fit residues: 174.9580
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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   64 VAL
Chi-restraints excluded: chain B residue  147 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0270
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
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 = 0.3146 r_free = 0.3146 target = 0.094542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.082465 restraints weight = 9968.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.13
r_work: 0.2850 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.3077

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= 0.208
  Angle     :  0.538   7.923   9471  Z= 0.276
  Chirality :  0.043   0.135   1034
  Planarity :  0.004   0.039   1234
  Dihedral  : 10.143 169.397    961
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.55 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.29), residues: 856
  helix:  1.29 (0.28), residues: 373
  sheet:  1.01 (0.42), residues: 149
  loop : -0.67 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A  28 
 PHE   0.020   0.001   PHE A 255 
 TYR   0.008   0.001   TYR A 103 
 ARG   0.004   0.000   ARG A 422 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5324.14 seconds
wall clock time: 94 minutes 56.70 seconds (5696.70 seconds total)