Starting phenix.real_space_refine
on Tue Apr 29 16:54:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv9_50793/04_2025/9fv9_50793.cif"
  }
  resolution = 3.6
  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=   0.013
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 5.56, per 1000 atoms: 0.63
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (123.76, 115.6, 140.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 1.88
  Conformation dependent library (CDL) restraints added in 957.2 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 7 sheets defined
      53.7% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 24
      removed outlier: 4.096A  pdb=" N   ALA A  21 " --> pdb=" O   PRO A  18 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
    Processing helix  chain 'A' and resid 25 through 30
      removed outlier: 3.992A  pdb=" N   VAL A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 4.062A  pdb=" N   LEU A  45 " --> pdb=" O   ASP A  41 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A  46 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 41 through 46'
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.800A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 3.553A  pdb=" N   PHE A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.178A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.623A  pdb=" N   ARG A 127 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 150
      removed outlier: 3.603A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 147 through 150'
    Processing helix  chain 'A' and resid 151 through 163
      removed outlier: 3.543A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   PHE A 161 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 209
      removed outlier: 3.661A  pdb=" N   SER A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 4.088A  pdb=" N   ILE A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 212
      No H-bonds generated for 'chain 'A' and resid 210 through 212'
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 235
    Processing helix  chain 'A' and resid 241 through 248
      removed outlier: 4.177A  pdb=" N   VAL A 245 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 270
      removed outlier: 3.875A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 292
      removed outlier: 3.874A  pdb=" N   MET A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
      removed outlier: 4.042A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 305
      No H-bonds generated for 'chain 'A' and resid 303 through 305'
    Processing helix  chain 'A' and resid 381 through 390
    Processing helix  chain 'A' and resid 411 through 417
      removed outlier: 3.588A  pdb=" N   ASN A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 446 through 457
      removed outlier: 3.759A  pdb=" N   ILE A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.850A  pdb=" N   GLN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 578
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 24 through 30
      removed outlier: 4.027A  pdb=" N   VAL B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.681A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 81
      removed outlier: 3.650A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.535A  pdb=" N   GLY B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU B  74 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ARG B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 88
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.700A  pdb=" N   GLY B 106 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   MET B 108 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   MET B 109 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   MET B 111 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 128
    Processing helix  chain 'B' and resid 133 through 138
      removed outlier: 3.545A  pdb=" N   SER B 138 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 149
    Processing helix  chain 'B' and resid 151 through 164
      removed outlier: 3.889A  pdb=" N   PHE B 161 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR B 163 " --> pdb=" O   MET B 159 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 210
      removed outlier: 3.530A  pdb=" N   SER B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE B 170 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 3.717A  pdb=" N   SER B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   THR B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   SER B 206 " --> pdb=" O   GLN B 202 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA B 207 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 218
      removed outlier: 3.807A  pdb=" N   LEU B 218 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 229
    Processing helix  chain 'B' and resid 230 through 239
      removed outlier: 3.695A  pdb=" N   ASN B 235 " --> pdb=" O   ASP B 231 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 249
    Processing helix  chain 'B' and resid 250 through 270
      removed outlier: 3.998A  pdb=" N   ALA B 262 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 289
    Processing helix  chain 'B' and resid 290 through 294
    Processing helix  chain 'B' and resid 295 through 300
      removed outlier: 3.657A  pdb=" N   SER B 300 " --> pdb=" O   ARG B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 304
    Processing helix  chain 'B' and resid 312 through 322
      removed outlier: 3.648A  pdb=" N   GLN B 316 " --> pdb=" O   MET B 312 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR B 320 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 390
      removed outlier: 4.193A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
      removed outlier: 3.570A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 3.578A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 527
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
      removed outlier: 4.095A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.511A  pdb=" N   VAL A 342 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349
      removed outlier: 5.978A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ASN A 361 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 532 through 536
      removed outlier: 6.174A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ALA A 536 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 536 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422
    Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 362
      removed outlier: 5.390A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 362
      removed outlier: 5.390A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 419 through 420
      removed outlier: 6.486A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    900 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: 2.22

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2760
        1.34 -     1.46: 1291
        1.46 -     1.57: 4794
        1.57 -     1.69: 1
        1.69 -     1.81: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" CA  ARG B 360 "
       pdb=" CB  ARG B 360 "
    ideal  model  delta    sigma   weight residual
    1.527  1.611 -0.084 2.48e-02 1.63e+03 1.14e+01
  bond pdb=" N   THR A 432 "
       pdb=" CA  THR A 432 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.32e-02 5.74e+03 8.57e+00
  bond pdb=" N   ILE B 172 "
       pdb=" CA  ILE B 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.21e-02 6.83e+03 8.46e+00
  bond pdb=" N   ILE A 389 "
       pdb=" CA  ILE A 389 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.31e+00
  bond pdb=" N   ILE B 170 "
       pdb=" CA  ILE B 170 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.17e-02 7.31e+03 8.19e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 11640
        2.45 -     4.89: 367
        4.89 -     7.34: 63
        7.34 -     9.78: 17
        9.78 -    12.23: 5
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     111.90  107.12    4.78 8.10e-01 1.52e+00 3.49e+01
  angle pdb=" N   ILE B 321 "
        pdb=" CA  ILE B 321 "
        pdb=" C   ILE B 321 "
      ideal   model   delta    sigma   weight residual
     110.72  105.06    5.66 1.01e+00 9.80e-01 3.14e+01
  angle pdb=" N   VAL A  32 "
        pdb=" CA  VAL A  32 "
        pdb=" C   VAL A  32 "
      ideal   model   delta    sigma   weight residual
     111.90  107.36    4.54 8.10e-01 1.52e+00 3.14e+01
  angle pdb=" CA  GLN B 240 "
        pdb=" CB  GLN B 240 "
        pdb=" CG  GLN B 240 "
      ideal   model   delta    sigma   weight residual
     114.10  124.28  -10.18 2.00e+00 2.50e-01 2.59e+01
  angle pdb=" N   ILE A 128 "
        pdb=" CA  ILE A 128 "
        pdb=" C   ILE A 128 "
      ideal   model   delta    sigma   weight residual
     112.12  107.97    4.15 8.40e-01 1.42e+00 2.44e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 4580
       16.90 -    33.79: 630
       33.79 -    50.69: 193
       50.69 -    67.58: 46
       67.58 -    84.48: 5
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  GLU B 476 "
           pdb=" C   GLU B 476 "
           pdb=" N   ASN B 477 "
           pdb=" CA  ASN B 477 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.06  -25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  MET B  75 "
           pdb=" C   MET B  75 "
           pdb=" N   ILE B  76 "
           pdb=" CA  ILE B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.36   24.64     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ASP B 277 "
           pdb=" C   ASP B 277 "
           pdb=" N   SER B 278 "
           pdb=" CA  SER B 278 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1131
       0.066 -    0.133: 257
       0.133 -    0.199: 40
       0.199 -    0.265: 10
       0.265 -    0.332: 2
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ASP B 323 "
            pdb=" N   ASP B 323 "
            pdb=" C   ASP B 323 "
            pdb=" CB  ASP B 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CB  ILE A 170 "
            pdb=" CA  ILE A 170 "
            pdb=" CG1 ILE A 170 "
            pdb=" CG2 ILE A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CB  ILE A 548 "
            pdb=" CA  ILE A 548 "
            pdb=" CG1 ILE A 548 "
            pdb=" CG2 ILE A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  21 "    0.057 5.00e-02 4.00e+02   8.62e-02 1.19e+01
        pdb=" N   PRO B  22 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO B  22 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B  22 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B  17 "    0.048 5.00e-02 4.00e+02   7.20e-02 8.28e+00
        pdb=" N   PRO B  18 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B  18 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  18 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 296 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.99e+00
        pdb=" N   PRO B 297 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 61
        2.61 -     3.18: 6969
        3.18 -     3.76: 13139
        3.76 -     4.33: 17176
        4.33 -     4.90: 28563
  Nonbonded interactions: 65908
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 511 "
            pdb=" CD1 LEU B 511 "
     model   vdw
     2.042 3.460
  nonbonded pdb=" O   THR B 280 "
            pdb=" OG1 THR B 280 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER B  93 "
            pdb=" OG  SER B  93 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LEU B 267 "
            pdb=" OG  SER B 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   THR A 339 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.324 3.040
  ... (remaining 65903 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.390
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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      :  0.006   0.084   8950  Z= 0.319
  Angle     :  1.068  12.231  12092  Z= 0.631
  Chirality :  0.060   0.332   1440
  Planarity :  0.007   0.086   1532
  Dihedral  : 17.476  84.476   3326
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.82 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 29.75 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.86 (0.21), residues: 1134
  helix: -2.97 (0.15), residues: 676
  sheet: -2.03 (0.68), residues: 42
  loop : -1.49 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B  66 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.031   0.002   PHE A  13 
 TYR   0.018   0.001   TYR A 445 
 ARG   0.013   0.001   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22695 (  316)
  hydrogen bonds       : angle       8.05446 (  900)
  covalent geometry    : bond        0.00551 ( 8950)
  covalent geometry    : angle       1.06757 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7933 (t0) cc_final: 0.7482 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2027
  time to fit residues: 39.3857
Evaluate side-chains
  112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0370
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.186653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.150666 restraints weight = 11864.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.148955 restraints weight = 16467.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.150703 restraints weight = 14573.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8950  Z= 0.122
  Angle     :  0.614  10.925  12092  Z= 0.318
  Chirality :  0.041   0.157   1440
  Planarity :  0.005   0.061   1532
  Dihedral  :  5.348  22.581   1238
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.38 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 26.86 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.57 (0.24), residues: 1134
  helix: -1.87 (0.19), residues: 642
  sheet: -1.77 (0.67), residues: 42
  loop : -1.15 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 107 
 PHE   0.014   0.001   PHE B 115 
 TYR   0.012   0.001   TYR A 130 
 ARG   0.008   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04663 (  316)
  hydrogen bonds       : angle       5.03498 (  900)
  covalent geometry    : bond        0.00263 ( 8950)
  covalent geometry    : angle       0.61447 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 120
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.7782 (t0) cc_final: 0.7378 (t0)
REVERT: A   66 TRP cc_start: 0.6018 (t60) cc_final: 0.5731 (m100)
REVERT: A   77 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (tt)
REVERT: A  160 MET cc_start: 0.8399 (mmm) cc_final: 0.8106 (ttm)
REVERT: A  471 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6792 (m-30)
REVERT: B   17 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7755 (t60)
REVERT: B  100 MET cc_start: 0.8347 (ttp) cc_final: 0.8085 (tmm)
REVERT: B  391 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7974 (ttt-90)
REVERT: B  471 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7137 (m-30)
  outliers start: 45
  outliers final: 20
  residues processed: 156
  average time/residue: 0.1784
  time to fit residues: 40.4774
Evaluate side-chains
  129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  391 ARG
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0370
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.184397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144678 restraints weight = 12039.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.142837 restraints weight = 13701.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.144535 restraints weight = 12570.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.137
  Angle     :  0.611   8.547  12092  Z= 0.314
  Chirality :  0.043   0.177   1440
  Planarity :  0.004   0.056   1532
  Dihedral  :  5.135  18.957   1238
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.20 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 27.89 %
    Favored  : 66.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.10 (0.25), residues: 1134
  helix: -1.50 (0.20), residues: 660
  sheet: -1.50 (0.70), residues: 42
  loop : -0.88 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.015   0.001   PHE B 116 
 TYR   0.011   0.001   TYR A 445 
 ARG   0.009   0.000   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  316)
  hydrogen bonds       : angle       4.68571 (  900)
  covalent geometry    : bond        0.00308 ( 8950)
  covalent geometry    : angle       0.61070 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 113
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   66 TRP cc_start: 0.6097 (t60) cc_final: 0.5829 (m100)
REVERT: A   77 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: A  160 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (ttm)
REVERT: A  177 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7591 (mt)
REVERT: A  223 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7414 (mt0)
REVERT: B   17 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7642 (t60)
REVERT: B  471 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7252 (m-30)
  outliers start: 52
  outliers final: 33
  residues processed: 157
  average time/residue: 0.1721
  time to fit residues: 39.0366
Evaluate side-chains
  141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 102
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  160 MET
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  553 ASP
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.0270
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0970
   chunk 39 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0770
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 GLN
B 579 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.187213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.151463 restraints weight = 11985.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.150785 restraints weight = 16654.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.152263 restraints weight = 14607.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8950  Z= 0.103
  Angle     :  0.567   8.327  12092  Z= 0.291
  Chirality :  0.041   0.146   1440
  Planarity :  0.004   0.052   1532
  Dihedral  :  4.831  18.323   1238
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.82 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.74 (0.25), residues: 1134
  helix: -1.15 (0.21), residues: 644
  sheet: -1.48 (0.70), residues: 42
  loop : -0.86 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  66 
 HIS   0.005   0.001   HIS B 576 
 PHE   0.011   0.001   PHE A  13 
 TYR   0.009   0.001   TYR A 445 
 ARG   0.008   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  316)
  hydrogen bonds       : angle       4.40662 (  900)
  covalent geometry    : bond        0.00213 ( 8950)
  covalent geometry    : angle       0.56682 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 110
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8328 (tt)
REVERT: A  177 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7453 (mt)
REVERT: A  218 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8605 (mp)
REVERT: A  223 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7329 (mt0)
REVERT: A  471 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7066 (m-30)
REVERT: B   17 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7590 (t60)
REVERT: B  138 SER cc_start: 0.8605 (m) cc_final: 0.8389 (p)
REVERT: B  471 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6917 (m-30)
  outliers start: 54
  outliers final: 31
  residues processed: 156
  average time/residue: 0.1757
  time to fit residues: 41.0508
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 108
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.4980
   chunk 35 optimal weight:   20.0000
   chunk 89 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 66 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.186017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.150327 restraints weight = 11944.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.148781 restraints weight = 17712.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.150786 restraints weight = 14222.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   8950  Z= 0.109
  Angle     :  0.571  10.842  12092  Z= 0.289
  Chirality :  0.041   0.140   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.708  17.564   1238
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 29.13 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.57 (0.26), residues: 1134
  helix: -1.01 (0.21), residues: 644
  sheet: -1.54 (0.70), residues: 42
  loop : -0.78 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.012   0.001   PHE B 116 
 TYR   0.021   0.001   TYR A 130 
 ARG   0.011   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  316)
  hydrogen bonds       : angle       4.25822 (  900)
  covalent geometry    : bond        0.00238 ( 8950)
  covalent geometry    : angle       0.57113 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 119
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8402 (tt)
REVERT: A  177 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7407 (mt)
REVERT: A  223 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7339 (mt0)
REVERT: A  411 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7470 (p)
REVERT: A  471 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7112 (m-30)
REVERT: B  138 SER cc_start: 0.8602 (m) cc_final: 0.8363 (p)
REVERT: B  466 MET cc_start: 0.6323 (ttt) cc_final: 0.5426 (mmm)
  outliers start: 49
  outliers final: 38
  residues processed: 161
  average time/residue: 0.1829
  time to fit residues: 42.5032
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 105
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 579 GLN
B 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144435 restraints weight = 11818.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143154 restraints weight = 13753.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.144568 restraints weight = 12487.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8950  Z= 0.152
  Angle     :  0.610   9.840  12092  Z= 0.308
  Chirality :  0.044   0.170   1440
  Planarity :  0.004   0.052   1532
  Dihedral  :  4.841  18.340   1238
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 29.24 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.57 (0.26), residues: 1134
  helix: -1.04 (0.21), residues: 656
  sheet: -1.57 (0.68), residues: 42
  loop : -0.70 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  66 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.015   0.001   PHE A  13 
 TYR   0.017   0.001   TYR B 445 
 ARG   0.013   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  316)
  hydrogen bonds       : angle       4.36296 (  900)
  covalent geometry    : bond        0.00355 ( 8950)
  covalent geometry    : angle       0.61028 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 110
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7605 (mt)
REVERT: A  223 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7400 (mt0)
REVERT: A  411 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7500 (p)
REVERT: A  471 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7415 (m-30)
REVERT: A  579 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6422 (tt0)
REVERT: B   17 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7636 (t60)
REVERT: B  138 SER cc_start: 0.8652 (m) cc_final: 0.8404 (p)
REVERT: B  397 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6139 (tm-30)
REVERT: B  466 MET cc_start: 0.6387 (ttt) cc_final: 0.5524 (mmm)
  outliers start: 58
  outliers final: 44
  residues processed: 157
  average time/residue: 0.1632
  time to fit residues: 38.1306
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain A residue  579 GLN
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 579 GLN
B 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.184316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.144253 restraints weight = 12036.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.142792 restraints weight = 14260.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.144707 restraints weight = 12085.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8950  Z= 0.124
  Angle     :  0.589   8.775  12092  Z= 0.298
  Chirality :  0.043   0.140   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.770  18.299   1238
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 30.06 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.53 (0.26), residues: 1134
  helix: -1.01 (0.21), residues: 656
  sheet: -1.58 (0.68), residues: 42
  loop : -0.67 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 576 
 PHE   0.016   0.001   PHE B 115 
 TYR   0.009   0.001   TYR A 445 
 ARG   0.012   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  316)
  hydrogen bonds       : angle       4.29583 (  900)
  covalent geometry    : bond        0.00279 ( 8950)
  covalent geometry    : angle       0.58891 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 109
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7603 (mt)
REVERT: A  223 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7379 (mt0)
REVERT: A  411 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7496 (p)
REVERT: A  471 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7465 (m-30)
REVERT: B   17 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7643 (t60)
REVERT: B  138 SER cc_start: 0.8631 (m) cc_final: 0.8383 (p)
REVERT: B  397 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6228 (tm-30)
REVERT: B  466 MET cc_start: 0.6527 (ttt) cc_final: 0.5749 (mmm)
REVERT: B  471 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7062 (m-30)
  outliers start: 51
  outliers final: 42
  residues processed: 151
  average time/residue: 0.1611
  time to fit residues: 36.8120
Evaluate side-chains
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.183289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.143020 restraints weight = 12172.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.141399 restraints weight = 14287.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.142436 restraints weight = 12061.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8950  Z= 0.126
  Angle     :  0.595   9.427  12092  Z= 0.301
  Chirality :  0.043   0.150   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.737  18.469   1238
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.20 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 29.65 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.51 (0.26), residues: 1134
  helix: -1.06 (0.21), residues: 672
  sheet: -1.59 (0.67), residues: 42
  loop : -0.50 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 576 
 PHE   0.030   0.001   PHE B 115 
 TYR   0.014   0.001   TYR B 445 
 ARG   0.013   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  316)
  hydrogen bonds       : angle       4.28752 (  900)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.59471 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 110
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7617 (mt)
REVERT: A  223 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7387 (mt0)
REVERT: A  411 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7476 (p)
REVERT: A  471 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7487 (m-30)
REVERT: B   17 TRP cc_start: 0.8382 (OUTLIER) cc_final: 0.7600 (t60)
REVERT: B   44 MET cc_start: 0.8633 (ttp) cc_final: 0.8403 (ttt)
REVERT: B  138 SER cc_start: 0.8646 (m) cc_final: 0.8399 (p)
REVERT: B  397 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6277 (tm-30)
REVERT: B  466 MET cc_start: 0.6568 (ttt) cc_final: 0.5796 (mmm)
REVERT: B  471 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7049 (m-30)
  outliers start: 56
  outliers final: 43
  residues processed: 157
  average time/residue: 0.1644
  time to fit residues: 38.6642
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 107
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0000
   chunk 79 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0170
   chunk 49 optimal weight:    0.0000
   chunk 32 optimal weight:   20.0000
   overall best weight:    0.3026

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

Flipped N/Q/H residues before XYZ refinement:
B 256 GLN
B 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.186199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.149285 restraints weight = 12042.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.147711 restraints weight = 16573.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.149513 restraints weight = 13491.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8950  Z= 0.102
  Angle     :  0.586   9.481  12092  Z= 0.295
  Chirality :  0.042   0.165   1440
  Planarity :  0.003   0.051   1532
  Dihedral  :  4.539  18.626   1238
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 31.20 %
    Favored  : 64.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.33 (0.26), residues: 1134
  helix: -0.87 (0.22), residues: 656
  sheet: -1.55 (0.68), residues: 42
  loop : -0.54 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 576 
 PHE   0.026   0.001   PHE B 115 
 TYR   0.010   0.001   TYR B 572 
 ARG   0.016   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  316)
  hydrogen bonds       : angle       4.19799 (  900)
  covalent geometry    : bond        0.00215 ( 8950)
  covalent geometry    : angle       0.58569 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7443 (mt)
REVERT: A  223 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7326 (mt0)
REVERT: A  471 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7193 (m-30)
REVERT: B   17 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7594 (t60)
REVERT: B   44 MET cc_start: 0.8516 (ttp) cc_final: 0.8241 (ttt)
REVERT: B  138 SER cc_start: 0.8647 (m) cc_final: 0.8445 (p)
REVERT: B  190 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7606 (mtm110)
REVERT: B  397 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6179 (tm-30)
REVERT: B  471 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6701 (m-30)
  outliers start: 43
  outliers final: 35
  residues processed: 147
  average time/residue: 0.1601
  time to fit residues: 35.4709
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
B 430 ASN
** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.186258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.150121 restraints weight = 11999.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148877 restraints weight = 16369.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.150201 restraints weight = 14099.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8950  Z= 0.109
  Angle     :  0.602  10.932  12092  Z= 0.300
  Chirality :  0.042   0.146   1440
  Planarity :  0.003   0.051   1532
  Dihedral  :  4.501  18.797   1238
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 31.30 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.25 (0.26), residues: 1134
  helix: -0.83 (0.21), residues: 660
  sheet: -0.89 (0.94), residues: 24
  loop : -0.55 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 576 
 PHE   0.025   0.001   PHE B 115 
 TYR   0.008   0.001   TYR B 572 
 ARG   0.016   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  316)
  hydrogen bonds       : angle       4.14786 (  900)
  covalent geometry    : bond        0.00240 ( 8950)
  covalent geometry    : angle       0.60246 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 107
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7390 (mt)
REVERT: A  223 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7332 (mt0)
REVERT: A  471 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7189 (m-30)
REVERT: B   17 TRP cc_start: 0.8243 (OUTLIER) cc_final: 0.7609 (t60)
REVERT: B  138 SER cc_start: 0.8635 (m) cc_final: 0.8425 (p)
REVERT: B  190 ARG cc_start: 0.7769 (ptp-170) cc_final: 0.7528 (mtm110)
REVERT: B  397 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6123 (tm-30)
REVERT: B  471 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6550 (m-30)
  outliers start: 41
  outliers final: 34
  residues processed: 142
  average time/residue: 0.1586
  time to fit residues: 33.9659
Evaluate side-chains
  143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  471 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0050
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0970
   chunk 54 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
B 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.187312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.150002 restraints weight = 12037.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.149104 restraints weight = 17979.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.151253 restraints weight = 13576.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8950  Z= 0.104
  Angle     :  0.591  10.692  12092  Z= 0.295
  Chirality :  0.042   0.151   1440
  Planarity :  0.003   0.051   1532
  Dihedral  :  4.381  18.839   1238
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.50 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 30.79 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.22 (0.26), residues: 1134
  helix: -0.78 (0.21), residues: 662
  sheet: -0.82 (0.95), residues: 24
  loop : -0.59 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 576 
 PHE   0.022   0.001   PHE B 115 
 TYR   0.006   0.001   TYR B 572 
 ARG   0.007   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  316)
  hydrogen bonds       : angle       4.10628 (  900)
  covalent geometry    : bond        0.00220 ( 8950)
  covalent geometry    : angle       0.59118 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3391.47 seconds
wall clock time: 59 minutes 50.05 seconds (3590.05 seconds total)