Starting phenix.real_space_refine
on Mon May 12 06:53:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv9_50793/05_2025/9fv9_50793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv9_50793/05_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_50793/05_2025/9fv9_50793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv9_50793/05_2025/9fv9_50793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv9_50793/05_2025/9fv9_50793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv9_50793/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.38, per 1000 atoms: 0.72
  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: 2.00
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.10
  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: 2.47

  Time building geometry restraints manager: 2.35 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:             6.750
  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:          0.420
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.080
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.570
-------------------------------------------------------------------------------
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  : 1.006 
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: 0.2058
  time to fit residues: 39.9096
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  : 1.018 
-------------------------------------------------------------------------------
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 = 0.150665 restraints weight = 11864.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148949 restraints weight = 16585.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.150691 restraints weight = 14572.506|
|-----------------------------------------------------------------------------|
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  10.924  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       5.03495 (  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  : 1.006 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.7782 (t0) cc_final: 0.7379 (t0)
REVERT: A   66 TRP cc_start: 0.6015 (t60) cc_final: 0.5732 (m100)
REVERT: A   77 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (tt)
REVERT: A  160 MET cc_start: 0.8394 (mmm) cc_final: 0.8102 (ttm)
REVERT: A  471 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6794 (m-30)
REVERT: B   17 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7753 (t60)
REVERT: B  100 MET cc_start: 0.8348 (ttp) cc_final: 0.8086 (tmm)
REVERT: B  391 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7973 (ttt-90)
REVERT: B  471 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7136 (m-30)
  outliers start: 45
  outliers final: 20
  residues processed: 156
  average time/residue: 0.1768
  time to fit residues: 40.0700
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  : 0.938 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0030
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 52 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.8792

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.184836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.144942 restraints weight = 12046.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.142942 restraints weight = 13037.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.144290 restraints weight = 11763.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.133
  Angle     :  0.608   8.557  12092  Z= 0.312
  Chirality :  0.043   0.197   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.120  19.026   1238
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 28.20 %
    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: -2.11 (0.25), residues: 1134
  helix: -1.51 (0.20), residues: 660
  sheet: -1.49 (0.70), residues: 42
  loop : -0.89 (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   0.012   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        0.04580 (  316)
  hydrogen bonds       : angle       4.70450 (  900)
  covalent geometry    : bond        0.00301 ( 8950)
  covalent geometry    : angle       0.60812 (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
  162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 113
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A   66 TRP cc_start: 0.6101 (t60) cc_final: 0.5804 (m100)
REVERT: A   77 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8259 (tt)
REVERT: A  160 MET cc_start: 0.8496 (mmm) cc_final: 0.8264 (ttm)
REVERT: A  177 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7525 (mt)
REVERT: A  223 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7409 (mt0)
REVERT: A  471 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7175 (m-30)
REVERT: B   17 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7626 (t60)
REVERT: B  471 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7219 (m-30)
  outliers start: 49
  outliers final: 31
  residues processed: 154
  average time/residue: 0.1838
  time to fit residues: 41.0580
Evaluate side-chains
  140 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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  146 VAL
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  327 GLU
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  471 ASP
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  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:    0.0020
   chunk 5 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0570
   chunk 39 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0000
   chunk 99 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.2110

-------------------------------------------------------------------------------
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 256 GLN
B 418 GLN
B 579 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.188133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.151890 restraints weight = 12051.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.149972 restraints weight = 19092.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.151932 restraints weight = 14621.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2021

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= 0.100
  Angle     :  0.565   9.185  12092  Z= 0.289
  Chirality :  0.041   0.142   1440
  Planarity :  0.004   0.060   1532
  Dihedral  :  4.776  18.267   1238
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 29.24 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.70 (0.25), residues: 1134
  helix: -1.12 (0.21), residues: 642
  sheet: -1.46 (0.71), residues: 42
  loop : -0.85 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  66 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.011   0.001   PHE A  13 
 TYR   0.008   0.001   TYR A 445 
 ARG   0.007   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  316)
  hydrogen bonds       : angle       4.38490 (  900)
  covalent geometry    : bond        0.00200 ( 8950)
  covalent geometry    : angle       0.56550 (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
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 114
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: A  177 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7349 (mt)
REVERT: A  223 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7280 (mt0)
REVERT: A  471 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7034 (m-30)
REVERT: B  391 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.8008 (ttt-90)
REVERT: B  471 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6811 (m-30)
  outliers start: 46
  outliers final: 24
  residues processed: 151
  average time/residue: 0.1840
  time to fit residues: 39.8748
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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   65 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 SER
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  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   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  391 ARG
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:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0770
   chunk 11 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.185662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.149337 restraints weight = 11943.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.147977 restraints weight = 17349.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.150140 restraints weight = 14178.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8950  Z= 0.116
  Angle     :  0.581  10.898  12092  Z= 0.294
  Chirality :  0.042   0.141   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  4.729  17.778   1238
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.62 %
    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: -1.58 (0.26), residues: 1134
  helix: -1.01 (0.21), residues: 644
  sheet: -1.53 (0.70), residues: 42
  loop : -0.79 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.008   0.001   HIS A 214 
 PHE   0.016   0.001   PHE B 116 
 TYR   0.022   0.001   TYR A 130 
 ARG   0.011   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  316)
  hydrogen bonds       : angle       4.29716 (  900)
  covalent geometry    : bond        0.00260 ( 8950)
  covalent geometry    : angle       0.58088 (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: 54
    poor density    : 114
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A   77 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: A  177 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7421 (mt)
REVERT: A  223 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7375 (mt0)
REVERT: A  411 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7494 (p)
REVERT: A  471 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7167 (m-30)
REVERT: B  190 ARG cc_start: 0.6881 (mtm110) cc_final: 0.6645 (mtm110)
REVERT: B  397 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6116 (tm-30)
REVERT: B  466 MET cc_start: 0.6267 (ttt) cc_final: 0.5357 (mmm)
  outliers start: 54
  outliers final: 37
  residues processed: 161
  average time/residue: 0.1766
  time to fit residues: 41.1104
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 105
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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  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  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  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  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   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  138 SER
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  419 VAL
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:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.185361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.145523 restraints weight = 11764.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.143992 restraints weight = 16196.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.145855 restraints weight = 14709.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8950  Z= 0.145
  Angle     :  0.602   9.534  12092  Z= 0.303
  Chirality :  0.043   0.149   1440
  Planarity :  0.004   0.049   1532
  Dihedral  :  4.811  18.468   1238
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 29.13 %
    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: -1.55 (0.26), residues: 1134
  helix: -1.02 (0.21), residues: 656
  sheet: -1.54 (0.69), residues: 42
  loop : -0.70 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.012   0.002   HIS B 576 
 PHE   0.014   0.001   PHE A  13 
 TYR   0.015   0.001   TYR B 445 
 ARG   0.010   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04279 (  316)
  hydrogen bonds       : angle       4.34384 (  900)
  covalent geometry    : bond        0.00334 ( 8950)
  covalent geometry    : angle       0.60213 (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
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 112
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7590 (mt)
REVERT: A  223 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7455 (mt0)
REVERT: A  411 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7516 (p)
REVERT: A  471 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7336 (m-30)
REVERT: A  579 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6389 (tt0)
REVERT: B  466 MET cc_start: 0.6378 (ttt) cc_final: 0.5526 (mmm)
  outliers start: 59
  outliers final: 46
  residues processed: 161
  average time/residue: 0.1736
  time to fit residues: 40.8714
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 105
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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   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  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  205 THR
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  327 GLU
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  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   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  138 SER
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  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:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0000
   chunk 30 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.8988

-------------------------------------------------------------------------------
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 = 0.4260 r_free = 0.4260 target = 0.188909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.150567 restraints weight = 11840.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.148751 restraints weight = 16372.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150290 restraints weight = 14094.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8950  Z= 0.132
  Angle     :  0.600   8.588  12092  Z= 0.305
  Chirality :  0.043   0.158   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  4.771  18.337   1238
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 29.65 %
    Favored  : 65.19 %
  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: -1.48 (0.26), residues: 1134
  helix: -0.97 (0.22), residues: 648
  sheet: -1.52 (0.68), residues: 42
  loop : -0.67 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.008   0.001   HIS A 214 
 PHE   0.016   0.001   PHE B 115 
 TYR   0.012   0.001   TYR A 445 
 ARG   0.012   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  316)
  hydrogen bonds       : angle       4.29885 (  900)
  covalent geometry    : bond        0.00300 ( 8950)
  covalent geometry    : angle       0.60023 (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
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 108
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7619 (mt)
REVERT: A  471 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7398 (m-30)
REVERT: B  397 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6072 (tm-30)
REVERT: B  466 MET cc_start: 0.6456 (ttt) cc_final: 0.5722 (mmm)
REVERT: B  471 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7021 (m-30)
  outliers start: 50
  outliers final: 44
  residues processed: 150
  average time/residue: 0.1667
  time to fit residues: 37.2726
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 104
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
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  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  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  327 GLU
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   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:    0.8980
   chunk 51 optimal weight:    0.0470
   chunk 85 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   chunk 99 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.185881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.146353 restraints weight = 11992.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.144600 restraints weight = 15720.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.146864 restraints weight = 12296.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.117
  Angle     :  0.586   7.855  12092  Z= 0.298
  Chirality :  0.042   0.148   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  4.669  18.570   1238
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 29.24 %
    Favored  : 65.29 %
  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: -1.41 (0.26), residues: 1134
  helix: -0.97 (0.21), residues: 660
  sheet: -1.43 (0.70), residues: 42
  loop : -0.53 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.007   0.001   HIS A 214 
 PHE   0.024   0.001   PHE B 115 
 TYR   0.013   0.001   TYR B 445 
 ARG   0.013   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  316)
  hydrogen bonds       : angle       4.21277 (  900)
  covalent geometry    : bond        0.00260 ( 8950)
  covalent geometry    : angle       0.58628 (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
  163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 110
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7569 (mt)
REVERT: A  411 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7469 (p)
REVERT: A  471 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (m-30)
REVERT: B  100 MET cc_start: 0.8188 (ttp) cc_final: 0.7971 (tmm)
REVERT: B  397 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6271 (tm-30)
REVERT: B  466 MET cc_start: 0.6541 (ttt) cc_final: 0.5795 (mmm)
  outliers start: 53
  outliers final: 43
  residues processed: 152
  average time/residue: 0.1540
  time to fit residues: 35.4007
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 105
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  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  205 THR
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  327 GLU
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   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  138 SER
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  442 THR
Chi-restraints excluded: chain B residue  470 LEU
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:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.182692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.144228 restraints weight = 11939.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.142123 restraints weight = 17219.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.143724 restraints weight = 14368.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8950  Z= 0.162
  Angle     :  0.632   8.050  12092  Z= 0.320
  Chirality :  0.045   0.164   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  4.850  18.820   1238
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.75 %
    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: -1.53 (0.26), residues: 1134
  helix: -1.07 (0.21), residues: 672
  sheet: -1.50 (0.68), residues: 42
  loop : -0.53 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  66 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.025   0.002   PHE B 115 
 TYR   0.014   0.001   TYR B 445 
 ARG   0.016   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04466 (  316)
  hydrogen bonds       : angle       4.39185 (  900)
  covalent geometry    : bond        0.00376 ( 8950)
  covalent geometry    : angle       0.63212 (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
  163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 108
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7703 (mt)
REVERT: A  411 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7454 (p)
REVERT: A  471 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7506 (m-30)
REVERT: B  100 MET cc_start: 0.8292 (ttp) cc_final: 0.8038 (tmm)
REVERT: B  190 ARG cc_start: 0.7874 (ptp-170) cc_final: 0.7487 (mtm110)
REVERT: B  397 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6221 (tm-30)
REVERT: B  471 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7134 (m-30)
  outliers start: 55
  outliers final: 45
  residues processed: 154
  average time/residue: 0.1617
  time to fit residues: 37.1960
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  : 0.894 
-------------------------------------------------------------------------------
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  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  205 THR
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  319 PHE
Chi-restraints excluded: chain A residue  327 GLU
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   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  138 SER
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  442 THR
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  562 HIS
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:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 87 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.185815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.147573 restraints weight = 11865.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.145615 restraints weight = 17057.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.148136 restraints weight = 13315.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8950  Z= 0.115
  Angle     :  0.603   8.289  12092  Z= 0.303
  Chirality :  0.043   0.194   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.677  18.721   1238
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 30.89 %
    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: -1.38 (0.26), residues: 1134
  helix: -0.91 (0.21), residues: 660
  sheet: -1.52 (0.68), residues: 42
  loop : -0.56 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.008   0.001   HIS B 576 
 PHE   0.023   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        0.04109 (  316)
  hydrogen bonds       : angle       4.25605 (  900)
  covalent geometry    : bond        0.00253 ( 8950)
  covalent geometry    : angle       0.60349 (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
  153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 110
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (mt)
REVERT: A  411 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7427 (p)
REVERT: A  471 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7253 (m-30)
REVERT: B  397 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6231 (tm-30)
  outliers start: 43
  outliers final: 40
  residues processed: 145
  average time/residue: 0.1562
  time to fit residues: 34.2104
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  : 0.913 
-------------------------------------------------------------------------------
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  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  205 THR
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  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   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  138 SER
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  470 LEU
Chi-restraints excluded: chain B residue  562 HIS
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 78 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 86 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 111 optimal weight:    0.0980
   chunk 102 optimal weight:    0.0060
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 562 HIS
B 430 ASN
** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.184899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.147907 restraints weight = 12012.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.146851 restraints weight = 17432.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.148834 restraints weight = 13701.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8950  Z= 0.112
  Angle     :  0.605   8.273  12092  Z= 0.304
  Chirality :  0.042   0.168   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.572  18.769   1238
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.99 %
    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: -1.32 (0.26), residues: 1134
  helix: -0.86 (0.21), residues: 660
  sheet: -1.63 (0.67), residues: 42
  loop : -0.52 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  66 
 HIS   0.006   0.001   HIS A 214 
 PHE   0.020   0.001   PHE B 115 
 TYR   0.013   0.001   TYR B 445 
 ARG   0.007   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  316)
  hydrogen bonds       : angle       4.21327 (  900)
  covalent geometry    : bond        0.00247 ( 8950)
  covalent geometry    : angle       0.60517 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2948.58 seconds
wall clock time: 53 minutes 10.08 seconds (3190.08 seconds total)