Starting phenix.real_space_refine
on Sat May  2 22:02:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rg7_19130/05_2026/8rg7_19130.cif"
  }
  resolution = 3.9
  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=   0.001 sd=   0.026
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      36      5.16       5
     C    5706      2.51       5
     N    1472      2.21       5
     O    1654      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8868
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'RHQ': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'RHQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.20, per 1000 atoms: 0.25
  Number of scatterers: 8868
  At special positions: 0
  Unit cell: (107.304, 87.316, 130.448, 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      36     16.00
     O    1654      8.00
     N    1472      7.00
     C    5706      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: 0.84
  Conformation dependent library (CDL) restraints added in 344.1 milliseconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      72.5% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 4.380A  pdb=" N   PHE A  15 " --> pdb=" O   LYS A  11 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 45
      removed outlier: 4.277A  pdb=" N   PHE A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 60
      removed outlier: 4.131A  pdb=" N   ASP A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   MET A  59 " --> pdb=" O   ASP A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 110
      removed outlier: 3.863A  pdb=" N   GLN A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER A  81 " --> pdb=" O   GLN A  77 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASN A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A 109 " --> pdb=" O   LYS A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.718A  pdb=" N   ASP A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 140
      removed outlier: 3.776A  pdb=" N   VAL A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   THR A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   MET A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 166 through 179
      removed outlier: 3.713A  pdb=" N   VAL A 174 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
    Processing helix  chain 'A' and resid 180 through 210
      removed outlier: 3.935A  pdb=" N   ILE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 219
      removed outlier: 3.542A  pdb=" N   VAL A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 275
      removed outlier: 3.922A  pdb=" N   GLY A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      Proline residue:  A 252  - end of helix
      removed outlier: 3.541A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 258 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 267 " --> pdb=" O   VAL A 263 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   TYR A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   MET A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLN A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 295
      removed outlier: 4.327A  pdb=" N   VAL A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 322
      removed outlier: 4.339A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   GLN A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS A 309 " --> pdb=" O   THR A 305 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 4.414A  pdb=" N   GLY A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 409 through 416
    Processing helix  chain 'A' and resid 431 through 437
    Processing helix  chain 'A' and resid 447 through 455
    Processing helix  chain 'A' and resid 457 through 462
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 4.195A  pdb=" N   ILE A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.769A  pdb=" N   ALA A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL A 523 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
      removed outlier: 3.779A  pdb=" N   VAL A 540 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 567
    Processing helix  chain 'A' and resid 568 through 581
      removed outlier: 4.446A  pdb=" N   GLU A 575 " --> pdb=" O   ARG A 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 22
      removed outlier: 4.359A  pdb=" N   PHE B  15 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   THR B  22 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 60
      removed outlier: 4.251A  pdb=" N   PHE B  31 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
      removed outlier: 3.808A  pdb=" N   GLN B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 110
      removed outlier: 3.974A  pdb=" N   LEU B  69 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN B  77 " --> pdb=" O   VAL B  73 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASN B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS B 109 " --> pdb=" O   LYS B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 3.812A  pdb=" N   ASN B 118 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 140
      removed outlier: 3.938A  pdb=" N   ASP B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR B 140 " --> pdb=" O   GLU B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
    Processing helix  chain 'B' and resid 166 through 179
      removed outlier: 3.670A  pdb=" N   VAL B 174 " --> pdb=" O   VAL B 170 " (cutoff:3.500A)
      Proline residue:  B 175  - end of helix
    Processing helix  chain 'B' and resid 180 through 210
      removed outlier: 3.773A  pdb=" N   ILE B 184 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 221 through 249
      removed outlier: 3.851A  pdb=" N   GLY B 227 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 275
      removed outlier: 3.848A  pdb=" N   MET B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY B 267 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   TYR B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   MET B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 322
      removed outlier: 4.240A  pdb=" N   VAL B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      Proline residue:  B 296  - end of helix
      removed outlier: 4.012A  pdb=" N   GLN B 299 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 329
      removed outlier: 4.364A  pdb=" N   THR B 328 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL B 329 " --> pdb=" O   GLU B 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 325 through 329'
    Processing helix  chain 'B' and resid 379 through 388
      removed outlier: 3.813A  pdb=" N   PHE B 384 " --> pdb=" O   LYS B 380 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LYS B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLU B 388 " --> pdb=" O   PHE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 407
    Processing helix  chain 'B' and resid 430 through 438
    Processing helix  chain 'B' and resid 441 through 447
      removed outlier: 4.457A  pdb=" N   THR B 444 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   ALA B 446 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 455
    Processing helix  chain 'B' and resid 456 through 462
      removed outlier: 4.252A  pdb=" N   PHE B 460 " --> pdb=" O   TYR B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 494
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 537 through 544
    Processing helix  chain 'B' and resid 559 through 567
      removed outlier: 3.600A  pdb=" N   LEU B 563 " --> pdb=" O   THR B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 581
      removed outlier: 3.785A  pdb=" N   GLU B 575 " --> pdb=" O   ARG B 571 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 364
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 421
      removed outlier: 6.623A  pdb=" N   THR A 370 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   PHE A 548 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 429 through 430
      removed outlier: 5.921A  pdb=" N   GLY A 429 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 360 through 365
      removed outlier: 5.435A  pdb=" N   VAL B 360 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   ILE B 341 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373
      removed outlier: 6.156A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 499 through 503
      removed outlier: 5.964A  pdb=" N   LEU B 500 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ILE B 533 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU B 502 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    580 hydrogen bonds defined for protein.
    1713 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: 1.26

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1448
        1.28 -     1.41: 2028
        1.41 -     1.54: 5424
        1.54 -     1.68: 38
        1.68 -     1.81: 70
  Bond restraints: 9008
  Sorted by residual:
  bond pdb=" C2  RHQ B 601 "
       pdb=" C3  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.419  1.152  0.267 2.00e-02 2.50e+03 1.78e+02
  bond pdb=" C2  RHQ A 601 "
       pdb=" C3  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.419  1.157  0.262 2.00e-02 2.50e+03 1.72e+02
  bond pdb=" C1  RHQ B 601 "
       pdb=" C2  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.421  1.193  0.228 2.00e-02 2.50e+03 1.30e+02
  bond pdb=" C1  RHQ A 601 "
       pdb=" C2  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.421  1.193  0.228 2.00e-02 2.50e+03 1.30e+02
  bond pdb=" C4  RHQ A 601 "
       pdb=" C5  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.431  1.650 -0.219 2.00e-02 2.50e+03 1.20e+02
  ... (remaining 9003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.40: 12181
       12.40 -    24.79: 5
       24.79 -    37.19: 8
       37.19 -    49.58: 0
       49.58 -    61.98: 2
  Bond angle restraints: 12196
  Sorted by residual:
  angle pdb=" C6  RHQ A 601 "
        pdb=" C5  RHQ A 601 "
        pdb=" N2  RHQ A 601 "
      ideal   model   delta    sigma   weight residual
     119.21   57.23   61.98 3.00e+00 1.11e-01 4.27e+02
  angle pdb=" C6  RHQ B 601 "
        pdb=" C5  RHQ B 601 "
        pdb=" N2  RHQ B 601 "
      ideal   model   delta    sigma   weight residual
     119.21   61.09   58.12 3.00e+00 1.11e-01 3.75e+02
  angle pdb=" CA  PRO B 404 "
        pdb=" N   PRO B 404 "
        pdb=" CD  PRO B 404 "
      ideal   model   delta    sigma   weight residual
     112.00   88.07   23.93 1.40e+00 5.10e-01 2.92e+02
  angle pdb=" C4  RHQ B 601 "
        pdb=" C5  RHQ B 601 "
        pdb=" N2  RHQ B 601 "
      ideal   model   delta    sigma   weight residual
     120.83  153.62  -32.79 3.00e+00 1.11e-01 1.19e+02
  angle pdb=" C14 RHQ B 601 "
        pdb=" C19 RHQ B 601 "
        pdb=" C26 RHQ B 601 "
      ideal   model   delta    sigma   weight residual
     119.09  148.72  -29.63 3.00e+00 1.11e-01 9.76e+01
  ... (remaining 12191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4885
       17.94 -    35.89: 454
       35.89 -    53.83: 63
       53.83 -    71.78: 17
       71.78 -    89.72: 7
  Dihedral angle restraints: 5426
    sinusoidal: 2150
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" C   PHE A  57 "
           pdb=" N   PHE A  57 "
           pdb=" CA  PHE A  57 "
           pdb=" CB  PHE A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.95  -15.65     0      2.50e+00 1.60e-01 3.92e+01
  dihedral pdb=" N   SER A  60 "
           pdb=" C   SER A  60 "
           pdb=" CA  SER A  60 "
           pdb=" CB  SER A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.14  -15.34     0      2.50e+00 1.60e-01 3.77e+01
  dihedral pdb=" C   SER A  60 "
           pdb=" N   SER A  60 "
           pdb=" CA  SER A  60 "
           pdb=" CB  SER A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.10   13.50     0      2.50e+00 1.60e-01 2.92e+01
  ... (remaining 5423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 1416
       0.115 -    0.230: 36
       0.230 -    0.345: 8
       0.345 -    0.460: 3
       0.460 -    0.575: 1
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CA  SER A  60 "
            pdb=" N   SER A  60 "
            pdb=" C   SER A  60 "
            pdb=" CB  SER A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.25e+00
  chirality pdb=" CA  PHE A  57 "
            pdb=" N   PHE A  57 "
            pdb=" C   PHE A  57 "
            pdb=" CB  PHE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.95   -0.44 2.00e-01 2.50e+01 4.93e+00
  chirality pdb=" CA  ILE B  67 "
            pdb=" N   ILE B  67 "
            pdb=" C   ILE B  67 "
            pdb=" CB  ILE B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.86   -0.42 2.00e-01 2.50e+01 4.47e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  50 "   -0.033 2.00e-02 2.50e+03   6.00e-02 3.60e+01
        pdb=" C   THR B  50 "    0.104 2.00e-02 2.50e+03
        pdb=" O   THR B  50 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   LYS B  51 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 402 "    0.029 2.00e-02 2.50e+03   5.96e-02 3.55e+01
        pdb=" C   ASP B 402 "   -0.103 2.00e-02 2.50e+03
        pdb=" O   ASP B 402 "    0.038 2.00e-02 2.50e+03
        pdb=" N   GLU B 403 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 403 "    0.108 5.00e-02 4.00e+02   1.44e-01 3.32e+01
        pdb=" N   PRO B 404 "   -0.248 5.00e-02 4.00e+02
        pdb=" CA  PRO B 404 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO B 404 "    0.077 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 136
        2.64 -     3.21: 9250
        3.21 -     3.77: 14115
        3.77 -     4.34: 18427
        4.34 -     4.90: 28498
  Nonbonded interactions: 70426
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 226 "
            pdb=" OE2 GLU B 101 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" OE2 GLU A 101 "
            pdb=" OH  TYR B 226 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ASP B 402 "
            pdb=" N   VAL B 405 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   LEU B 524 "
            pdb=" NH2 ARG B 528 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   LYS B 245 "
            pdb=" OG  SER B 248 "
     model   vdw
     2.246 3.040
  ... (remaining 70421 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:             1.520
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.970
  Find NCS groups from input model:        0.140
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
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      :  0.009   0.267   9008  Z= 0.537
  Angle     :  1.465  61.979  12196  Z= 0.690
  Chirality :  0.056   0.575   1464
  Planarity :  0.007   0.144   1526
  Dihedral  : 14.150  89.724   3322
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  8.60 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  0.62 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.19 %
  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 are not related in a simple way.
  whole: -1.26 (0.25), residues: 1140
  helix:  0.00 (0.20), residues: 723
  sheet:  0.58 (0.68), residues: 61
  loop : -2.80 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 126 
 TYR   0.019   0.002   TYR A  86 
 PHE   0.032   0.002   PHE A 160 
 TRP   0.008   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00946 ( 9008)
  covalent geometry    : angle       1.46490 (12196)
  hydrogen bonds       : bond        0.18192 (  580)
  hydrogen bonds       : angle       7.95836 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 217
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7880 (mmt) cc_final: 0.7653 (ptp)
REVERT: A  106 LYS cc_start: 0.9291 (tppt) cc_final: 0.9066 (tppt)
REVERT: A  162 MET cc_start: 0.8454 (ttt) cc_final: 0.8092 (tmm)
REVERT: A  271 MET cc_start: 0.7122 (mtm) cc_final: 0.6832 (mtm)
REVERT: A  326 GLU cc_start: 0.8049 (pm20) cc_final: 0.7814 (pm20)
REVERT: A  439 LEU cc_start: 0.8341 (mp) cc_final: 0.6969 (tp)
REVERT: A  548 PHE cc_start: 0.8908 (t80) cc_final: 0.8482 (t80)
REVERT: B  500 LEU cc_start: 0.8766 (mm) cc_final: 0.8544 (mm)
REVERT: B  573 PHE cc_start: 0.8888 (m-10) cc_final: 0.8656 (p90)
  outliers start: 5
  outliers final: 3
  residues processed: 221
  average time/residue: 0.0738
  time to fit residues: 24.0675
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  404 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
B  91 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.120975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.085893 restraints weight = 23761.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.088476 restraints weight = 14394.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090274 restraints weight = 10287.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.091421 restraints weight = 8136.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.092327 restraints weight = 6939.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9008  Z= 0.290
  Angle     :  0.936  13.554  12196  Z= 0.454
  Chirality :  0.047   0.224   1464
  Planarity :  0.006   0.155   1526
  Dihedral  :  8.131  59.630   1248
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.93 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 14.52 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.73 (0.25), residues: 1140
  helix:  0.44 (0.20), residues: 738
  sheet:  0.91 (0.72), residues: 54
  loop : -2.74 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 484 
 TYR   0.029   0.002   TYR B 226 
 PHE   0.017   0.002   PHE A  57 
 TRP   0.006   0.002   TRP B 413 
 HIS   0.005   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 9008)
  covalent geometry    : angle       0.93560 (12196)
  hydrogen bonds       : bond        0.05805 (  580)
  hydrogen bonds       : angle       5.76544 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9528 (m) cc_final: 0.9254 (t)
REVERT: A   83 TYR cc_start: 0.8848 (t80) cc_final: 0.8561 (t80)
REVERT: A  259 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (mmp)
REVERT: A  271 MET cc_start: 0.7541 (mtm) cc_final: 0.7283 (mtm)
REVERT: A  326 GLU cc_start: 0.8119 (pm20) cc_final: 0.7818 (pm20)
REVERT: A  385 LYS cc_start: 0.9267 (mtmt) cc_final: 0.8976 (mttp)
REVERT: A  387 LEU cc_start: 0.9337 (mm) cc_final: 0.9038 (mm)
REVERT: A  454 MET cc_start: 0.8525 (mtt) cc_final: 0.8322 (mtm)
REVERT: A  548 PHE cc_start: 0.8893 (t80) cc_final: 0.8297 (t80)
REVERT: A  564 MET cc_start: 0.5519 (tpt) cc_final: 0.5245 (tpt)
REVERT: B  271 MET cc_start: 0.7440 (ptm) cc_final: 0.7069 (ptm)
REVERT: B  339 LEU cc_start: 0.9069 (mm) cc_final: 0.8835 (tt)
  outliers start: 40
  outliers final: 26
  residues processed: 183
  average time/residue: 0.0772
  time to fit residues: 20.9835
Evaluate side-chains
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.0070
   chunk 80 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0060
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0070
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.2432

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.125969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.090652 restraints weight = 22762.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.093371 restraints weight = 13854.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095247 restraints weight = 9840.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.096543 restraints weight = 7720.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097335 restraints weight = 6513.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   9008  Z= 0.157
  Angle     :  0.787  11.490  12196  Z= 0.383
  Chirality :  0.044   0.215   1464
  Planarity :  0.005   0.141   1526
  Dihedral  :  7.558  55.196   1242
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.67 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.98 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.36 (0.26), residues: 1140
  helix:  0.79 (0.20), residues: 738
  sheet:  0.55 (0.69), residues: 59
  loop : -2.71 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.017   0.002   TYR B 226 
 PHE   0.016   0.001   PHE A 573 
 TRP   0.005   0.001   TRP B 413 
 HIS   0.001   0.000   HIS B 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9008)
  covalent geometry    : angle       0.78674 (12196)
  hydrogen bonds       : bond        0.04811 (  580)
  hydrogen bonds       : angle       5.15316 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASN cc_start: 0.4450 (OUTLIER) cc_final: 0.3857 (p0)
REVERT: A  250 VAL cc_start: 0.9066 (t) cc_final: 0.8807 (p)
REVERT: A  259 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (mmp)
REVERT: A  271 MET cc_start: 0.7409 (mtm) cc_final: 0.7149 (mtm)
REVERT: A  387 LEU cc_start: 0.9288 (mm) cc_final: 0.8966 (mm)
REVERT: A  427 MET cc_start: 0.5274 (ppp) cc_final: 0.5041 (ppp)
REVERT: A  439 LEU cc_start: 0.8212 (mp) cc_final: 0.6756 (tp)
REVERT: A  548 PHE cc_start: 0.8774 (t80) cc_final: 0.8379 (t80)
REVERT: A  564 MET cc_start: 0.5338 (tpt) cc_final: 0.5098 (tpt)
REVERT: A  573 PHE cc_start: 0.8926 (m-80) cc_final: 0.8132 (m-80)
REVERT: B  271 MET cc_start: 0.7352 (ptm) cc_final: 0.6839 (ptm)
REVERT: B  387 LEU cc_start: 0.9449 (mm) cc_final: 0.9147 (mm)
REVERT: B  564 MET cc_start: 0.5193 (mmt) cc_final: 0.4967 (mmm)
  outliers start: 28
  outliers final: 19
  residues processed: 196
  average time/residue: 0.0671
  time to fit residues: 20.3973
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 100 optimal weight:    9.9990
   chunk 24 optimal weight:    0.3980
   chunk 92 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.124511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.088528 restraints weight = 23580.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.091341 restraints weight = 14195.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.093247 restraints weight = 10034.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.094595 restraints weight = 7866.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.095428 restraints weight = 6594.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   9008  Z= 0.162
  Angle     :  0.773  11.079  12196  Z= 0.377
  Chirality :  0.043   0.200   1464
  Planarity :  0.005   0.132   1526
  Dihedral  :  7.497  59.164   1242
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.93 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.95 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.23 (0.26), residues: 1140
  helix:  0.90 (0.20), residues: 735
  sheet:  0.49 (0.69), residues: 59
  loop : -2.62 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 389 
 TYR   0.016   0.001   TYR B 114 
 PHE   0.011   0.001   PHE A 390 
 TRP   0.019   0.002   TRP B 413 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9008)
  covalent geometry    : angle       0.77316 (12196)
  hydrogen bonds       : bond        0.04535 (  580)
  hydrogen bonds       : angle       5.06974 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 164
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASN cc_start: 0.4344 (OUTLIER) cc_final: 0.4128 (t0)
REVERT: A  259 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (mmp)
REVERT: A  271 MET cc_start: 0.7526 (mtm) cc_final: 0.7247 (mtm)
REVERT: A  387 LEU cc_start: 0.9281 (mm) cc_final: 0.8976 (mm)
REVERT: A  408 TYR cc_start: 0.8318 (t80) cc_final: 0.8115 (t80)
REVERT: A  427 MET cc_start: 0.5472 (ppp) cc_final: 0.5238 (ppp)
REVERT: A  439 LEU cc_start: 0.8413 (mp) cc_final: 0.7081 (tp)
REVERT: A  548 PHE cc_start: 0.8806 (t80) cc_final: 0.8388 (t80)
REVERT: A  564 MET cc_start: 0.5197 (tpt) cc_final: 0.4982 (tpt)
REVERT: A  573 PHE cc_start: 0.8966 (m-80) cc_final: 0.8166 (m-80)
REVERT: B  271 MET cc_start: 0.7315 (ptm) cc_final: 0.6874 (ptm)
REVERT: B  387 LEU cc_start: 0.9517 (mm) cc_final: 0.9299 (mm)
REVERT: B  441 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7673 (tpt90)
  outliers start: 39
  outliers final: 30
  residues processed: 190
  average time/residue: 0.0717
  time to fit residues: 20.4777
Evaluate side-chains
  181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3908 r_free = 0.3908 target = 0.124540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.089967 restraints weight = 22879.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.092133 restraints weight = 14149.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.093939 restraints weight = 9274.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.095187 restraints weight = 7379.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.095342 restraints weight = 6330.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   9008  Z= 0.153
  Angle     :  0.756  10.875  12196  Z= 0.369
  Chirality :  0.043   0.193   1464
  Planarity :  0.005   0.127   1526
  Dihedral  :  7.273  54.080   1242
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.84 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 21.27 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.19 (0.26), residues: 1140
  helix:  0.93 (0.20), residues: 738
  sheet:  0.33 (0.65), residues: 64
  loop : -2.65 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 345 
 TYR   0.016   0.001   TYR B 114 
 PHE   0.011   0.001   PHE A  57 
 TRP   0.018   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9008)
  covalent geometry    : angle       0.75614 (12196)
  hydrogen bonds       : bond        0.04357 (  580)
  hydrogen bonds       : angle       4.94859 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 168
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.8520 (t0) cc_final: 0.8313 (t0)
REVERT: A  163 ASN cc_start: 0.4263 (OUTLIER) cc_final: 0.4037 (t0)
REVERT: A  271 MET cc_start: 0.7515 (mtm) cc_final: 0.7227 (mtm)
REVERT: A  387 LEU cc_start: 0.9300 (mm) cc_final: 0.8974 (mm)
REVERT: A  427 MET cc_start: 0.5538 (ppp) cc_final: 0.5295 (ppp)
REVERT: A  439 LEU cc_start: 0.8387 (mp) cc_final: 0.7060 (tp)
REVERT: A  548 PHE cc_start: 0.8819 (t80) cc_final: 0.8387 (t80)
REVERT: B  271 MET cc_start: 0.7299 (ptm) cc_final: 0.6835 (ptm)
REVERT: B  387 LEU cc_start: 0.9535 (mm) cc_final: 0.9315 (mm)
REVERT: B  441 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7687 (tpt90)
  outliers start: 45
  outliers final: 34
  residues processed: 199
  average time/residue: 0.0623
  time to fit residues: 19.1653
Evaluate side-chains
  188 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 112 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.123179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.088186 restraints weight = 23029.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.090831 restraints weight = 13642.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.093123 restraints weight = 8983.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.093433 restraints weight = 6791.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.093579 restraints weight = 6324.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9008  Z= 0.173
  Angle     :  0.769  11.238  12196  Z= 0.375
  Chirality :  0.043   0.188   1464
  Planarity :  0.005   0.122   1526
  Dihedral  :  6.985  47.871   1242
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.93 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 22.51 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.22 (0.26), residues: 1140
  helix:  0.94 (0.20), residues: 737
  sheet:  0.61 (0.67), residues: 59
  loop : -2.74 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.019   0.002   TYR B 114 
 PHE   0.023   0.001   PHE A 390 
 TRP   0.014   0.001   TRP B 413 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 9008)
  covalent geometry    : angle       0.76882 (12196)
  hydrogen bonds       : bond        0.04296 (  580)
  hydrogen bonds       : angle       4.94603 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 155
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.8492 (t0) cc_final: 0.8241 (t0)
REVERT: A  163 ASN cc_start: 0.4497 (OUTLIER) cc_final: 0.4202 (t0)
REVERT: A  271 MET cc_start: 0.7602 (mtm) cc_final: 0.7353 (mmm)
REVERT: A  387 LEU cc_start: 0.9283 (mm) cc_final: 0.8962 (mm)
REVERT: A  427 MET cc_start: 0.5653 (ppp) cc_final: 0.5377 (ppp)
REVERT: A  439 LEU cc_start: 0.8441 (mp) cc_final: 0.7131 (tp)
REVERT: A  501 MET cc_start: 0.9035 (mtp) cc_final: 0.8597 (mtm)
REVERT: A  548 PHE cc_start: 0.8817 (t80) cc_final: 0.8379 (t80)
REVERT: A  573 PHE cc_start: 0.8901 (m-80) cc_final: 0.8195 (m-80)
REVERT: B  271 MET cc_start: 0.7252 (ptm) cc_final: 0.6200 (ptm)
  outliers start: 53
  outliers final: 38
  residues processed: 196
  average time/residue: 0.0658
  time to fit residues: 19.9749
Evaluate side-chains
  186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 76 optimal weight:    0.4980
   chunk 48 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0970
   chunk 37 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3900 r_free = 0.3900 target = 0.123988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.087976 restraints weight = 23116.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.090658 restraints weight = 14129.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092467 restraints weight = 10071.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.093727 restraints weight = 7942.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.094529 restraints weight = 6730.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9008  Z= 0.152
  Angle     :  0.760  11.872  12196  Z= 0.370
  Chirality :  0.043   0.186   1464
  Planarity :  0.005   0.118   1526
  Dihedral  :  6.721  47.466   1242
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.11 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 23.65 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.19 (0.26), residues: 1140
  helix:  0.94 (0.20), residues: 740
  sheet:  0.57 (0.68), residues: 59
  loop : -2.70 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 441 
 TYR   0.017   0.001   TYR B 114 
 PHE   0.034   0.001   PHE A  57 
 TRP   0.016   0.001   TRP B 413 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9008)
  covalent geometry    : angle       0.75961 (12196)
  hydrogen bonds       : bond        0.04254 (  580)
  hydrogen bonds       : angle       4.88566 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 159
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.8502 (t0) cc_final: 0.8247 (t0)
REVERT: A  163 ASN cc_start: 0.4376 (OUTLIER) cc_final: 0.4134 (t0)
REVERT: A  259 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (mmp)
REVERT: A  271 MET cc_start: 0.7590 (mtm) cc_final: 0.7343 (mmm)
REVERT: A  387 LEU cc_start: 0.9277 (mm) cc_final: 0.8952 (mm)
REVERT: A  427 MET cc_start: 0.5565 (ppp) cc_final: 0.5341 (ppp)
REVERT: A  439 LEU cc_start: 0.8379 (mp) cc_final: 0.7109 (tp)
REVERT: A  548 PHE cc_start: 0.8812 (t80) cc_final: 0.8393 (t80)
REVERT: A  573 PHE cc_start: 0.8897 (m-80) cc_final: 0.8164 (m-80)
REVERT: B  271 MET cc_start: 0.7570 (ptm) cc_final: 0.7149 (ptm)
REVERT: B  387 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9316 (mm)
REVERT: B  525 MET cc_start: 0.7240 (pmm) cc_final: 0.6955 (pmm)
  outliers start: 49
  outliers final: 39
  residues processed: 194
  average time/residue: 0.0626
  time to fit residues: 19.1284
Evaluate side-chains
  194 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0040
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.125125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.089576 restraints weight = 22765.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.092184 restraints weight = 13978.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094037 restraints weight = 9993.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.095340 restraints weight = 7850.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.096193 restraints weight = 6606.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9008  Z= 0.143
  Angle     :  0.753  12.670  12196  Z= 0.365
  Chirality :  0.043   0.189   1464
  Planarity :  0.005   0.115   1526
  Dihedral  :  6.396  46.485   1242
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.19 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 24.07 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.07 (0.26), residues: 1140
  helix:  1.08 (0.20), residues: 740
  sheet:  0.62 (0.70), residues: 59
  loop : -2.78 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.019   0.002   TYR A 350 
 PHE   0.026   0.001   PHE A  57 
 TRP   0.018   0.001   TRP B 413 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9008)
  covalent geometry    : angle       0.75271 (12196)
  hydrogen bonds       : bond        0.04067 (  580)
  hydrogen bonds       : angle       4.81651 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.8353 (t0) cc_final: 0.8016 (t0)
REVERT: A  163 ASN cc_start: 0.4240 (OUTLIER) cc_final: 0.4017 (t0)
REVERT: A  259 MET cc_start: 0.9054 (mmp) cc_final: 0.8813 (mmp)
REVERT: A  357 LEU cc_start: 0.8883 (tp) cc_final: 0.8605 (pp)
REVERT: A  387 LEU cc_start: 0.9247 (mm) cc_final: 0.8865 (mm)
REVERT: A  439 LEU cc_start: 0.8399 (mp) cc_final: 0.7177 (tp)
REVERT: A  548 PHE cc_start: 0.8802 (t80) cc_final: 0.8389 (t80)
REVERT: A  573 PHE cc_start: 0.8939 (m-80) cc_final: 0.8220 (m-80)
REVERT: B  271 MET cc_start: 0.7412 (ptm) cc_final: 0.7044 (ptm)
REVERT: B  387 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9295 (mm)
  outliers start: 45
  outliers final: 37
  residues processed: 200
  average time/residue: 0.0677
  time to fit residues: 20.7842
Evaluate side-chains
  196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0770
   chunk 12 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.125025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.089589 restraints weight = 22916.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.092225 restraints weight = 13999.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094070 restraints weight = 9991.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095381 restraints weight = 7842.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.096165 restraints weight = 6604.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9008  Z= 0.149
  Angle     :  0.792  17.479  12196  Z= 0.380
  Chirality :  0.043   0.186   1464
  Planarity :  0.005   0.113   1526
  Dihedral  :  6.395  46.545   1242
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.19 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 25.41 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.14 (0.26), residues: 1140
  helix:  1.04 (0.20), residues: 737
  sheet:  0.63 (0.72), residues: 59
  loop : -2.82 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 389 
 TYR   0.015   0.001   TYR B 114 
 PHE   0.019   0.001   PHE A  57 
 TRP   0.009   0.001   TRP B 413 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9008)
  covalent geometry    : angle       0.79211 (12196)
  hydrogen bonds       : bond        0.04099 (  580)
  hydrogen bonds       : angle       4.83269 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 166
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASN cc_start: 0.4336 (OUTLIER) cc_final: 0.4046 (t0)
REVERT: A  271 MET cc_start: 0.6902 (mmm) cc_final: 0.6580 (mmm)
REVERT: A  387 LEU cc_start: 0.9240 (mm) cc_final: 0.8878 (mm)
REVERT: A  439 LEU cc_start: 0.8434 (mp) cc_final: 0.7178 (tp)
REVERT: A  501 MET cc_start: 0.8797 (mtp) cc_final: 0.8241 (mmm)
REVERT: A  548 PHE cc_start: 0.8836 (t80) cc_final: 0.8413 (t80)
REVERT: A  564 MET cc_start: 0.5126 (tpt) cc_final: 0.4924 (tpt)
REVERT: A  573 PHE cc_start: 0.8945 (m-80) cc_final: 0.8206 (m-80)
REVERT: B  271 MET cc_start: 0.7427 (ptm) cc_final: 0.7053 (ptm)
REVERT: B  387 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9321 (mm)
  outliers start: 48
  outliers final: 40
  residues processed: 200
  average time/residue: 0.0674
  time to fit residues: 20.5625
Evaluate side-chains
  199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0970
   chunk 102 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.123818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087680 restraints weight = 23444.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.090262 restraints weight = 14673.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.092051 restraints weight = 10635.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.093272 restraints weight = 8462.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094057 restraints weight = 7219.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9008  Z= 0.167
  Angle     :  0.809  17.482  12196  Z= 0.388
  Chirality :  0.044   0.202   1464
  Planarity :  0.005   0.111   1526
  Dihedral  :  6.460  49.646   1242
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.54 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 25.93 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.17 (0.26), residues: 1140
  helix:  0.99 (0.20), residues: 740
  sheet:  0.61 (0.72), residues: 59
  loop : -2.79 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 484 
 TYR   0.019   0.002   TYR A 350 
 PHE   0.015   0.001   PHE A  57 
 TRP   0.010   0.002   TRP A 104 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9008)
  covalent geometry    : angle       0.80928 (12196)
  hydrogen bonds       : bond        0.04125 (  580)
  hydrogen bonds       : angle       4.82961 ( 1713)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 161
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASN cc_start: 0.4434 (OUTLIER) cc_final: 0.4175 (t0)
REVERT: A  271 MET cc_start: 0.6939 (mmm) cc_final: 0.6605 (mmm)
REVERT: A  387 LEU cc_start: 0.9250 (mm) cc_final: 0.8893 (mm)
REVERT: A  439 LEU cc_start: 0.8481 (mp) cc_final: 0.7270 (tp)
REVERT: A  500 LEU cc_start: 0.9176 (tt) cc_final: 0.8759 (mp)
REVERT: A  501 MET cc_start: 0.8907 (mtp) cc_final: 0.8127 (mmm)
REVERT: A  548 PHE cc_start: 0.8883 (t80) cc_final: 0.8416 (t80)
REVERT: A  573 PHE cc_start: 0.8961 (m-80) cc_final: 0.8265 (m-80)
REVERT: B  271 MET cc_start: 0.7372 (ptm) cc_final: 0.6595 (ptm)
REVERT: B  387 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9333 (mm)
  outliers start: 46
  outliers final: 38
  residues processed: 196
  average time/residue: 0.0722
  time to fit residues: 21.6180
Evaluate side-chains
  198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 158
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  163 ASN
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  559 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   74 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  567 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 560 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.124124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.087923 restraints weight = 23141.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.090601 restraints weight = 14043.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.092481 restraints weight = 9991.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.093753 restraints weight = 7857.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.094455 restraints weight = 6645.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9008  Z= 0.157
  Angle     :  0.808  16.603  12196  Z= 0.388
  Chirality :  0.044   0.210   1464
  Planarity :  0.005   0.110   1526
  Dihedral  :  6.349  48.188   1242
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.19 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 26.66 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -0.18 (0.26), residues: 1140
  helix:  0.99 (0.20), residues: 741
  sheet:  0.57 (0.73), residues: 59
  loop : -2.81 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.017   0.001   TYR B 114 
 PHE   0.010   0.001   PHE A 390 
 TRP   0.008   0.001   TRP A 104 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9008)
  covalent geometry    : angle       0.80784 (12196)
  hydrogen bonds       : bond        0.04155 (  580)
  hydrogen bonds       : angle       4.81648 ( 1713)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1477.45 seconds
wall clock time: 26 minutes 18.44 seconds (1578.44 seconds total)