Starting phenix.real_space_refine
on Wed Sep 17 13:04:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv9_50793/09_2025/9fv9_50793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv9_50793/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv9_50793/09_2025/9fv9_50793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv9_50793/09_2025/9fv9_50793.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fv9_50793/09_2025/9fv9_50793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv9_50793/09_2025/9fv9_50793.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.28, per 1000 atoms: 0.26
  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: 0.81
  Conformation dependent library (CDL) restraints added in 375.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 7 sheets defined
      53.7% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  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: 1.46

  Time building geometry restraints manager: 1.08 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: 0.02
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:             4.410
  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:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.860
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
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 : 4.02
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.013   0.001   ARG B 190 
 TYR   0.018   0.001   TYR A 445 
 PHE   0.031   0.002   PHE A  13 
 TRP   0.037   0.003   TRP B  66 
 HIS   0.005   0.001   HIS A 214 

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

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.358 
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: 0.0988
  time to fit residues: 19.2567
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  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0030
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.7396

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.186240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.150714 restraints weight = 12011.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.149551 restraints weight = 16955.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.151038 restraints weight = 15843.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.150285 restraints weight = 11355.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.151122 restraints weight = 11604.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8950  Z= 0.126
  Angle     :  0.624  10.966  12092  Z= 0.324
  Chirality :  0.042   0.161   1440
  Planarity :  0.005   0.062   1532
  Dihedral  :  5.421  22.304   1238
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.56 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 26.76 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.24), residues: 1134
  helix: -1.96 (0.19), residues: 660
  sheet: -1.84 (0.66), residues: 42
  loop : -1.08 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 190 
 TYR   0.013   0.001   TYR A 130 
 PHE   0.012   0.001   PHE A  13 
 TRP   0.023   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8950)
  covalent geometry    : angle       0.62394 (12092)
  hydrogen bonds       : bond        0.04901 (  316)
  hydrogen bonds       : angle       5.11235 (  900)

*********************** 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
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.7795 (t0) cc_final: 0.7360 (t0)
REVERT: A   66 TRP cc_start: 0.6070 (t60) cc_final: 0.5706 (m100)
REVERT: A   77 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8276 (tt)
REVERT: A  160 MET cc_start: 0.8425 (mmm) cc_final: 0.8170 (ttm)
REVERT: A  471 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6874 (m-30)
REVERT: B   17 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7765 (t60)
REVERT: B  100 MET cc_start: 0.8364 (ttp) cc_final: 0.8098 (tmm)
REVERT: B  190 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6556 (mtm110)
REVERT: B  471 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7222 (m-30)
  outliers start: 43
  outliers final: 19
  residues processed: 154
  average time/residue: 0.0718
  time to fit residues: 16.2794
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   71 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  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  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 51 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0170
   chunk 96 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
A 485 GLN
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 HIS
B 579 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.185538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.149702 restraints weight = 12050.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.149307 restraints weight = 17095.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150514 restraints weight = 15241.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.150156 restraints weight = 9755.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.150915 restraints weight = 9400.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.118
  Angle     :  0.591   8.198  12092  Z= 0.306
  Chirality :  0.042   0.187   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.108  19.217   1238
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.79 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.25), residues: 1134
  helix: -1.46 (0.20), residues: 648
  sheet: -1.56 (0.69), residues: 42
  loop : -0.95 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 190 
 TYR   0.010   0.001   TYR A 445 
 PHE   0.011   0.001   PHE A 115 
 TRP   0.018   0.002   TRP B  66 
 HIS   0.002   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8950)
  covalent geometry    : angle       0.59144 (12092)
  hydrogen bonds       : bond        0.04464 (  316)
  hydrogen bonds       : angle       4.73273 (  900)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 115
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   71 VAL cc_start: 0.8204 (p) cc_final: 0.7991 (p)
REVERT: A   77 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8239 (tt)
REVERT: A  177 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7514 (mt)
REVERT: A  223 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7387 (mt0)
REVERT: A  471 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6994 (m-30)
REVERT: B   17 TRP cc_start: 0.8277 (OUTLIER) cc_final: 0.7686 (t60)
REVERT: B  391 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8001 (ttt-90)
REVERT: B  471 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7059 (m-30)
  outliers start: 50
  outliers final: 30
  residues processed: 159
  average time/residue: 0.0833
  time to fit residues: 19.3003
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  : 0.332 
-------------------------------------------------------------------------------
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  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  553 ASP
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0370
   chunk 81 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.187825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.152842 restraints weight = 12125.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.152935 restraints weight = 16970.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.154314 restraints weight = 14363.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.153885 restraints weight = 9264.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.154656 restraints weight = 9025.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2029

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= 0.102
  Angle     :  0.566   8.430  12092  Z= 0.290
  Chirality :  0.041   0.161   1440
  Planarity :  0.004   0.052   1532
  Dihedral  :  4.813  18.459   1238
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 28.72 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.25), residues: 1134
  helix: -1.12 (0.21), residues: 642
  sheet: -1.45 (0.70), residues: 42
  loop : -0.87 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 190 
 TYR   0.020   0.001   TYR A 130 
 PHE   0.011   0.001   PHE A  13 
 TRP   0.017   0.001   TRP B  66 
 HIS   0.007   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8950)
  covalent geometry    : angle       0.56575 (12092)
  hydrogen bonds       : bond        0.03986 (  316)
  hydrogen bonds       : angle       4.42194 (  900)

*********************** 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
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 113
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   71 VAL cc_start: 0.8166 (p) cc_final: 0.7953 (p)
REVERT: A   77 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8373 (tt)
REVERT: A  177 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (mt)
REVERT: A  223 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7324 (mt0)
REVERT: A  471 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.7004 (m-30)
REVERT: B   17 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7733 (t60)
REVERT: B  391 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.8025 (ttt-90)
REVERT: B  471 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6876 (m-30)
  outliers start: 46
  outliers final: 30
  residues processed: 152
  average time/residue: 0.0752
  time to fit residues: 16.9833
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
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  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  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  553 ASP
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  135 VAL
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 96 optimal weight:    6.9990
   chunk 111 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0010
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6386

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.189454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.150694 restraints weight = 12009.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.149524 restraints weight = 15061.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.151672 restraints weight = 13276.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.151332 restraints weight = 8548.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.152119 restraints weight = 8555.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8950  Z= 0.111
  Angle     :  0.568   8.378  12092  Z= 0.290
  Chirality :  0.041   0.146   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.714  18.695   1238
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 28.10 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.26), residues: 1134
  helix: -1.00 (0.21), residues: 644
  sheet: -1.52 (0.69), residues: 42
  loop : -0.79 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 190 
 TYR   0.013   0.001   TYR A 445 
 PHE   0.009   0.001   PHE A 230 
 TRP   0.017   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8950)
  covalent geometry    : angle       0.56764 (12092)
  hydrogen bonds       : bond        0.03989 (  316)
  hydrogen bonds       : angle       4.30866 (  900)

*********************** 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
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 113
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: A  177 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7459 (mt)
REVERT: A  218 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: A  223 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7316 (mt0)
REVERT: A  471 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7267 (m-30)
REVERT: B  391 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (ttt-90)
REVERT: B  397 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6245 (tm-30)
REVERT: B  466 MET cc_start: 0.6457 (ttt) cc_final: 0.5454 (mmm)
  outliers start: 58
  outliers final: 39
  residues processed: 164
  average time/residue: 0.0787
  time to fit residues: 18.9929
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 106
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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   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  145 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  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   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  391 ARG
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  442 THR
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 109 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 579 GLN
B 256 GLN
B 576 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.183542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.144159 restraints weight = 11949.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143297 restraints weight = 16053.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.145249 restraints weight = 13791.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.144961 restraints weight = 9143.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.145401 restraints weight = 9492.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8950  Z= 0.161
  Angle     :  0.618  11.357  12092  Z= 0.312
  Chirality :  0.045   0.235   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.899  18.696   1238
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 28.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.26), residues: 1134
  helix: -1.10 (0.21), residues: 660
  sheet: -1.55 (0.67), residues: 42
  loop : -0.69 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 190 
 TYR   0.012   0.001   TYR A 445 
 PHE   0.015   0.001   PHE A  13 
 TRP   0.016   0.002   TRP B  66 
 HIS   0.007   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8950)
  covalent geometry    : angle       0.61811 (12092)
  hydrogen bonds       : bond        0.04446 (  316)
  hydrogen bonds       : angle       4.44703 (  900)

*********************** 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
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 106
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7682 (mt)
REVERT: A  223 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7399 (mt0)
REVERT: A  471 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7475 (m-30)
REVERT: A  579 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6446 (tt0)
REVERT: B   17 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7546 (t60)
REVERT: B  391 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7928 (ttt-90)
  outliers start: 61
  outliers final: 45
  residues processed: 161
  average time/residue: 0.0767
  time to fit residues: 18.5178
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  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  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  474 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain A residue  579 GLN
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  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  305 ASN
Chi-restraints excluded: chain B residue  391 ARG
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  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 88 optimal weight:   40.0000
   chunk 65 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.186209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.148387 restraints weight = 11949.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148039 restraints weight = 12897.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.149628 restraints weight = 11756.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149270 restraints weight = 8356.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.149649 restraints weight = 9505.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8950  Z= 0.121
  Angle     :  0.597   9.844  12092  Z= 0.303
  Chirality :  0.043   0.163   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.767  19.193   1238
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 30.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.26), residues: 1134
  helix: -0.94 (0.22), residues: 644
  sheet: -1.57 (0.67), residues: 42
  loop : -0.72 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 190 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.014   0.001   PHE A 580 
 TRP   0.017   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8950)
  covalent geometry    : angle       0.59679 (12092)
  hydrogen bonds       : bond        0.04199 (  316)
  hydrogen bonds       : angle       4.31205 (  900)

*********************** 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  : 0.299 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7645 (mt)
REVERT: A  223 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7385 (mt0)
REVERT: A  471 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7398 (m-30)
REVERT: B   17 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7523 (t60)
REVERT: B  391 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7912 (ttt-90)
REVERT: B  397 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6052 (tm-30)
REVERT: B  471 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6896 (m-30)
  outliers start: 50
  outliers final: 39
  residues processed: 153
  average time/residue: 0.0743
  time to fit residues: 16.8943
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 101
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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  177 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   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  391 ARG
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  471 ASP
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 18 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0670
   chunk 99 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4238 r_free = 0.4238 target = 0.186547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.147794 restraints weight = 11915.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.146319 restraints weight = 16342.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.149035 restraints weight = 12426.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.148361 restraints weight = 8566.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.149038 restraints weight = 8769.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8950  Z= 0.111
  Angle     :  0.589   8.700  12092  Z= 0.300
  Chirality :  0.042   0.144   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.636  18.446   1238
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 30.37 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.26), residues: 1134
  helix: -0.93 (0.22), residues: 656
  sheet: -1.60 (0.67), residues: 42
  loop : -0.59 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 190 
 TYR   0.024   0.001   TYR A 130 
 PHE   0.014   0.001   PHE A  13 
 TRP   0.017   0.001   TRP B  66 
 HIS   0.005   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8950)
  covalent geometry    : angle       0.58906 (12092)
  hydrogen bonds       : bond        0.03987 (  316)
  hydrogen bonds       : angle       4.25331 (  900)

*********************** 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
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 108
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: A  223 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7332 (mt0)
REVERT: A  471 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7314 (m-30)
REVERT: B   17 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7588 (t60)
REVERT: B  391 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7955 (ttt-90)
REVERT: B  397 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6258 (tm-30)
REVERT: B  471 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6723 (m-30)
  outliers start: 52
  outliers final: 39
  residues processed: 153
  average time/residue: 0.0725
  time to fit residues: 16.9195
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 103
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  343 GLU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  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  391 ARG
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  471 ASP
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 109 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.184049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144941 restraints weight = 11924.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143750 restraints weight = 16894.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.146004 restraints weight = 14288.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145602 restraints weight = 9560.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.146116 restraints weight = 9890.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2677

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= 0.142
  Angle     :  0.615   7.946  12092  Z= 0.311
  Chirality :  0.044   0.206   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.764  18.506   1238
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 30.58 %
    Favored  : 63.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.26), residues: 1134
  helix: -1.03 (0.21), residues: 672
  sheet: -1.61 (0.66), residues: 42
  loop : -0.53 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 530 
 TYR   0.014   0.001   TYR B 572 
 PHE   0.011   0.001   PHE A 189 
 TRP   0.015   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8950)
  covalent geometry    : angle       0.61489 (12092)
  hydrogen bonds       : bond        0.04238 (  316)
  hydrogen bonds       : angle       4.31020 (  900)

*********************** 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
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 106
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7671 (mt)
REVERT: A  223 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7371 (mt0)
REVERT: A  471 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7372 (m-30)
REVERT: B   17 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7592 (t60)
REVERT: B  100 MET cc_start: 0.8303 (ttp) cc_final: 0.8048 (tmm)
REVERT: B  190 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7398 (mtm110)
REVERT: B  391 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7929 (ttt-90)
REVERT: B  397 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6260 (tm-30)
  outliers start: 53
  outliers final: 45
  residues processed: 150
  average time/residue: 0.0688
  time to fit residues: 16.0391
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 105
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  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  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  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  111 MET
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  391 ARG
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 108 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.185282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.146344 restraints weight = 11941.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.144898 restraints weight = 13923.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.145999 restraints weight = 12547.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.146167 restraints weight = 9445.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.146580 restraints weight = 8848.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8950  Z= 0.124
  Angle     :  0.604   8.555  12092  Z= 0.305
  Chirality :  0.043   0.174   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.712  18.700   1238
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 31.10 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.26), residues: 1134
  helix: -0.95 (0.21), residues: 660
  sheet: -1.58 (0.67), residues: 42
  loop : -0.58 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 530 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.015   0.001   PHE A  13 
 TRP   0.016   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8950)
  covalent geometry    : angle       0.60445 (12092)
  hydrogen bonds       : bond        0.04161 (  316)
  hydrogen bonds       : angle       4.27128 (  900)

********************** 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
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  177 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7694 (mt)
REVERT: A  208 GLU cc_start: 0.6905 (tp30) cc_final: 0.6655 (tp30)
REVERT: A  223 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7359 (mt0)
REVERT: A  471 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7323 (m-30)
REVERT: B   17 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7606 (t60)
REVERT: B  100 MET cc_start: 0.8242 (ttp) cc_final: 0.8021 (tmm)
REVERT: B  190 ARG cc_start: 0.7748 (ptp-170) cc_final: 0.7358 (mtm110)
REVERT: B  391 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (ttt-90)
REVERT: B  397 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6195 (tm-30)
REVERT: B  471 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6771 (m-30)
  outliers start: 51
  outliers final: 43
  residues processed: 148
  average time/residue: 0.0764
  time to fit residues: 17.0668
Evaluate side-chains
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  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  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  356 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   93 SER
Chi-restraints excluded: chain B residue   96 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  391 ARG
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  442 THR
Chi-restraints excluded: chain B residue  471 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 29 optimal weight:    0.3980
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   chunk 65 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0770
   overall best weight:    0.3938

-------------------------------------------------------------------------------
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 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.187959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.148362 restraints weight = 11771.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146993 restraints weight = 13758.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.148181 restraints weight = 12700.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.148675 restraints weight = 8387.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.148969 restraints weight = 8351.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8950  Z= 0.104
  Angle     :  0.590   8.402  12092  Z= 0.295
  Chirality :  0.042   0.165   1440
  Planarity :  0.003   0.051   1532
  Dihedral  :  4.484  18.620   1238
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 31.92 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.26), residues: 1134
  helix: -0.82 (0.22), residues: 656
  sheet: -0.93 (0.93), residues: 24
  loop : -0.66 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 360 
 TYR   0.007   0.001   TYR B 572 
 PHE   0.006   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8950)
  covalent geometry    : angle       0.58955 (12092)
  hydrogen bonds       : bond        0.03729 (  316)
  hydrogen bonds       : angle       4.12089 (  900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1605.78 seconds
wall clock time: 28 minutes 25.76 seconds (1705.76 seconds total)