Starting phenix.real_space_refine
on Mon May 12 08:19:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuw_50780/05_2025/9fuw_50780.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.37, per 1000 atoms: 0.72
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (121.04, 111.52, 140.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      68.4% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 21
      removed outlier: 3.879A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 55
      removed outlier: 4.534A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 107
      Proline residue:  B  68  - end of helix
      removed outlier: 3.593A  pdb=" N   VAL B  92 " --> pdb=" O   CYS B  88 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.670A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 164
      removed outlier: 3.503A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 212
      Proline residue:  B 176  - end of helix
      removed outlier: 4.095A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 250
    Processing helix  chain 'B' and resid 251 through 272
    Processing helix  chain 'B' and resid 280 through 294
      removed outlier: 3.757A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 305 through 307
      No H-bonds generated for 'chain 'B' and resid 305 through 307'
    Processing helix  chain 'B' and resid 310 through 323
    Processing helix  chain 'B' and resid 381 through 391
      removed outlier: 3.586A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.664A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
    Processing helix  chain 'A' and resid 16 through 21
      removed outlier: 3.902A  pdb=" N   ILE A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 54
      removed outlier: 3.674A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ASP A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A  45 " --> pdb=" O   ASP A  41 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 65 through 107
      removed outlier: 3.837A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A  92 " --> pdb=" O   CYS A  88 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   THR A  99 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.995A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 146
      removed outlier: 4.478A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 163
      removed outlier: 3.815A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ILE A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 3.640A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.770A  pdb=" N   ASN A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   MET A 200 " --> pdb=" O   MET A 196 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 250
    Processing helix  chain 'A' and resid 250 through 272
      removed outlier: 3.670A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 302
      removed outlier: 3.901A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
    Processing helix  chain 'A' and resid 303 through 323
      removed outlier: 3.616A  pdb=" N   GLN A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 3.938A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.760A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 529
      removed outlier: 4.445A  pdb=" N   ASN A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 544
      removed outlier: 3.592A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 568
      removed outlier: 3.663A  pdb=" N   HIS A 568 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 579
    Processing sheet with id=AA1, first strand: chain 'B' and resid 401 through 402
    Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.977A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 548 through 551
      removed outlier: 6.602A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 345
      removed outlier: 4.063A  pdb=" N   ARG A 345 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLU A 399 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.143A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)

    544 hydrogen bonds defined for protein.
    1614 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2110
        1.33 -     1.45: 1695
        1.45 -     1.58: 5040
        1.58 -     1.70: 1
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   ILE B  20 "
       pdb=" CA  ILE B  20 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.27e+00
  bond pdb=" N   ARG A  14 "
       pdb=" CA  ARG A  14 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.041 1.35e-02 5.49e+03 9.07e+00
  bond pdb=" N   THR B 283 "
       pdb=" CA  THR B 283 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.21e+00
  bond pdb=" N   ALA B  21 "
       pdb=" CA  ALA B  21 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.04e-02 9.25e+03 7.98e+00
  bond pdb=" N   GLN A 309 "
       pdb=" CA  GLN A 309 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.24e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11727
        1.89 -     3.78: 308
        3.78 -     5.67: 46
        5.67 -     7.55: 8
        7.55 -     9.44: 3
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   PHE A 308 "
        pdb=" CA  PHE A 308 "
        pdb=" C   PHE A 308 "
      ideal   model   delta    sigma   weight residual
     111.28  102.00    9.28 1.09e+00 8.42e-01 7.25e+01
  angle pdb=" N   ARG A 310 "
        pdb=" CA  ARG A 310 "
        pdb=" C   ARG A 310 "
      ideal   model   delta    sigma   weight residual
     111.07  104.00    7.07 1.07e+00 8.73e-01 4.37e+01
  angle pdb=" CA  PHE A  13 "
        pdb=" C   PHE A  13 "
        pdb=" O   PHE A  13 "
      ideal   model   delta    sigma   weight residual
     120.82  114.46    6.36 1.05e+00 9.07e-01 3.67e+01
  angle pdb=" N   PHE A  13 "
        pdb=" CA  PHE A  13 "
        pdb=" C   PHE A  13 "
      ideal   model   delta    sigma   weight residual
     111.07  117.25   -6.18 1.07e+00 8.73e-01 3.33e+01
  angle pdb=" N   ALA A 314 "
        pdb=" CA  ALA A 314 "
        pdb=" C   ALA A 314 "
      ideal   model   delta    sigma   weight residual
     111.28  105.30    5.98 1.09e+00 8.42e-01 3.01e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4673
       17.90 -    35.81: 586
       35.81 -    53.71: 160
       53.71 -    71.62: 24
       71.62 -    89.52: 11
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  ARG B  14 "
           pdb=" C   ARG B  14 "
           pdb=" N   ARG B  15 "
           pdb=" CA  ARG B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.29   28.71     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" C   PHE A 308 "
           pdb=" N   PHE A 308 "
           pdb=" CA  PHE A 308 "
           pdb=" CB  PHE A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.85  -13.75     0      2.50e+00 1.60e-01 3.02e+01
  dihedral pdb=" C   THR A  12 "
           pdb=" N   THR A  12 "
           pdb=" CA  THR A  12 "
           pdb=" CB  THR A  12 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.88   11.88     0      2.50e+00 1.60e-01 2.26e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1339
       0.079 -    0.159: 93
       0.159 -    0.238: 3
       0.238 -    0.318: 0
       0.318 -    0.397: 5
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ARG A  14 "
            pdb=" N   ARG A  14 "
            pdb=" C   ARG A  14 "
            pdb=" CB  ARG A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  LEU A  16 "
            pdb=" N   LEU A  16 "
            pdb=" C   LEU A  16 "
            pdb=" CB  LEU A  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.53e+00
  chirality pdb=" CA  PHE A 308 "
            pdb=" N   PHE A 308 "
            pdb=" C   PHE A 308 "
            pdb=" CB  PHE A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.14e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 351 "   -0.039 5.00e-02 4.00e+02   5.83e-02 5.45e+00
        pdb=" N   PRO A 352 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 352 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 352 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  13 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   PHE A  13 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PHE A  13 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A  14 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 307 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.24e+00
        pdb=" C   GLN A 307 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLN A 307 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A 308 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1593
        2.76 -     3.29: 9860
        3.29 -     3.83: 15065
        3.83 -     4.36: 16926
        4.36 -     4.90: 28110
  Nonbonded interactions: 71554
  Sorted by model distance:
  nonbonded pdb=" O   THR A 123 "
            pdb=" OG  SER A 126 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NH1 ARG B  61 "
            pdb=" O   SER A 271 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ILE B 128 "
            pdb=" OG  SER B 132 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   GLN B 202 "
            pdb=" OG1 THR B 205 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD1 ASN B 198 "
            pdb=" N   THR B 199 "
     model   vdw
     2.254 3.120
  ... (remaining 71549 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.490
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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      :  0.004   0.045   8950  Z= 0.232
  Angle     :  0.730   9.442  12092  Z= 0.454
  Chirality :  0.045   0.397   1440
  Planarity :  0.004   0.058   1532
  Dihedral  : 17.186  89.522   3326
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.73 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 30.99 %
    Favored  : 68.70 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 1134
  helix:  0.66 (0.19), residues: 752
  sheet: -3.38 (0.96), residues: 24
  loop : -1.37 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 562 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.011   0.001   TYR A 410 
 ARG   0.008   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13865 (  544)
  hydrogen bonds       : angle       6.29488 ( 1614)
  covalent geometry    : bond        0.00408 ( 8950)
  covalent geometry    : angle       0.73035 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: B  458 TYR cc_start: 0.8501 (m-80) cc_final: 0.8278 (m-10)
  outliers start: 3
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1953
  time to fit residues: 36.1826
Evaluate side-chains
  118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:   10.0000
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.110157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.083426 restraints weight = 25407.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.086056 restraints weight = 12851.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.087787 restraints weight = 8302.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   8950  Z= 0.154
  Angle     :  0.644   8.534  12092  Z= 0.333
  Chirality :  0.042   0.158   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  4.927  35.030   1241
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 27.79 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1134
  helix:  1.03 (0.19), residues: 768
  sheet: -3.21 (0.97), residues: 24
  loop : -1.25 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A 562 
 PHE   0.018   0.002   PHE A  56 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.006   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  544)
  hydrogen bonds       : angle       4.76009 ( 1614)
  covalent geometry    : bond        0.00360 ( 8950)
  covalent geometry    : angle       0.64380 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7472 (mtt180)
REVERT: B  312 MET cc_start: 0.4702 (tpt) cc_final: 0.3925 (tpt)
REVERT: B  458 TYR cc_start: 0.8471 (m-80) cc_final: 0.8229 (m-10)
REVERT: A  324 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7947 (t)
REVERT: A  402 MET cc_start: 0.7855 (tpt) cc_final: 0.7552 (tpt)
REVERT: A  456 MET cc_start: 0.8577 (mmm) cc_final: 0.8267 (ttt)
REVERT: A  578 MET cc_start: 0.6396 (ptp) cc_final: 0.6033 (ppp)
  outliers start: 29
  outliers final: 18
  residues processed: 158
  average time/residue: 0.1704
  time to fit residues: 39.5513
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  237 MET
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 417 ASN
A 418 GLN
** A 436 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.112962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.086822 restraints weight = 25606.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.089620 restraints weight = 12426.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.091428 restraints weight = 7824.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   8950  Z= 0.130
  Angle     :  0.600  10.169  12092  Z= 0.307
  Chirality :  0.040   0.166   1440
  Planarity :  0.004   0.034   1532
  Dihedral  :  4.610  20.283   1238
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.93 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1134
  helix:  1.12 (0.19), residues: 772
  sheet: -2.97 (1.03), residues: 24
  loop : -1.25 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 562 
 PHE   0.013   0.001   PHE A 462 
 TYR   0.015   0.001   TYR B 572 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  544)
  hydrogen bonds       : angle       4.49505 ( 1614)
  covalent geometry    : bond        0.00304 ( 8950)
  covalent geometry    : angle       0.59968 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7179 (mmt180)
REVERT: B  219 ILE cc_start: 0.9594 (tp) cc_final: 0.9294 (mm)
REVERT: B  312 MET cc_start: 0.4676 (tpt) cc_final: 0.4099 (tpt)
REVERT: B  458 TYR cc_start: 0.8360 (m-80) cc_final: 0.8154 (m-10)
REVERT: A  170 ILE cc_start: 0.9267 (tp) cc_final: 0.8876 (tp)
REVERT: A  402 MET cc_start: 0.7856 (tpt) cc_final: 0.7622 (mmm)
REVERT: A  456 MET cc_start: 0.8532 (mmm) cc_final: 0.8186 (ttt)
  outliers start: 36
  outliers final: 19
  residues processed: 165
  average time/residue: 0.1744
  time to fit residues: 41.8221
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  237 MET
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  374 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  541 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    0.6980
   chunk 39 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   chunk 107 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
A 427 HIS
A 436 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.111252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.084867 restraints weight = 25456.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.087518 restraints weight = 12734.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.089246 restraints weight = 8175.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   8950  Z= 0.160
  Angle     :  0.618   9.596  12092  Z= 0.316
  Chirality :  0.041   0.181   1440
  Planarity :  0.004   0.030   1532
  Dihedral  :  4.573  18.906   1238
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 29.03 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1134
  helix:  1.17 (0.19), residues: 782
  sheet: -3.01 (1.01), residues: 24
  loop : -1.21 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.020   0.002   PHE B 115 
 TYR   0.032   0.002   TYR A 439 
 ARG   0.006   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  544)
  hydrogen bonds       : angle       4.45841 ( 1614)
  covalent geometry    : bond        0.00375 ( 8950)
  covalent geometry    : angle       0.61819 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7383 (mpp80)
REVERT: B  174 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8651 (mp)
REVERT: B  312 MET cc_start: 0.4707 (tpt) cc_final: 0.4016 (tpt)
REVERT: A  170 ILE cc_start: 0.9305 (tp) cc_final: 0.8919 (tp)
REVERT: A  456 MET cc_start: 0.8560 (mmm) cc_final: 0.8313 (mmm)
REVERT: A  466 MET cc_start: 0.8386 (mmm) cc_final: 0.8017 (mmt)
REVERT: A  480 LEU cc_start: 0.9050 (tp) cc_final: 0.8779 (tt)
  outliers start: 42
  outliers final: 29
  residues processed: 161
  average time/residue: 0.1853
  time to fit residues: 42.9265
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.109956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.082954 restraints weight = 25718.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085627 restraints weight = 13138.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.087354 restraints weight = 8537.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8950  Z= 0.189
  Angle     :  0.643   8.152  12092  Z= 0.331
  Chirality :  0.042   0.140   1440
  Planarity :  0.004   0.032   1532
  Dihedral  :  4.675  18.557   1238
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.20 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.24 %
    Favored  : 66.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1134
  helix:  1.15 (0.19), residues: 782
  sheet: -3.10 (1.00), residues: 24
  loop : -1.36 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.034   0.002   PHE A 349 
 TYR   0.027   0.002   TYR A 439 
 ARG   0.008   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  544)
  hydrogen bonds       : angle       4.53294 ( 1614)
  covalent geometry    : bond        0.00438 ( 8950)
  covalent geometry    : angle       0.64299 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 132
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7415 (mpp80)
REVERT: B  312 MET cc_start: 0.4841 (tpt) cc_final: 0.4166 (tpt)
REVERT: A  170 ILE cc_start: 0.9326 (tp) cc_final: 0.8936 (tp)
REVERT: A  339 THR cc_start: 0.8522 (m) cc_final: 0.8129 (p)
REVERT: A  456 MET cc_start: 0.8544 (mmm) cc_final: 0.8239 (mmm)
REVERT: A  480 LEU cc_start: 0.9073 (tp) cc_final: 0.8798 (tt)
  outliers start: 44
  outliers final: 29
  residues processed: 161
  average time/residue: 0.1815
  time to fit residues: 42.4552
Evaluate side-chains
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.112167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.085672 restraints weight = 25546.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.088391 restraints weight = 12914.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.090186 restraints weight = 8324.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.108   8950  Z= 0.135
  Angle     :  0.626  11.361  12092  Z= 0.315
  Chirality :  0.041   0.145   1440
  Planarity :  0.003   0.030   1532
  Dihedral  :  4.569  18.114   1238
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 30.99 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1134
  helix:  1.20 (0.19), residues: 782
  sheet: -3.05 (0.99), residues: 24
  loop : -1.36 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.036   0.002   PHE A 462 
 TYR   0.016   0.002   TYR B 572 
 ARG   0.009   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  544)
  hydrogen bonds       : angle       4.36347 ( 1614)
  covalent geometry    : bond        0.00317 ( 8950)
  covalent geometry    : angle       0.62641 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  410 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7581 (m-80)
REVERT: A  170 ILE cc_start: 0.9311 (tp) cc_final: 0.8933 (tp)
REVERT: A  324 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7709 (t)
REVERT: A  339 THR cc_start: 0.8497 (m) cc_final: 0.8091 (p)
REVERT: A  349 PHE cc_start: 0.7647 (t80) cc_final: 0.6633 (t80)
REVERT: A  456 MET cc_start: 0.8524 (mmm) cc_final: 0.8013 (tpt)
REVERT: A  480 LEU cc_start: 0.9050 (tp) cc_final: 0.8712 (tt)
REVERT: A  481 LEU cc_start: 0.8792 (mt) cc_final: 0.8464 (mt)
  outliers start: 30
  outliers final: 22
  residues processed: 153
  average time/residue: 0.1764
  time to fit residues: 39.3480
Evaluate side-chains
  141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.4980
   chunk 100 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 435 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.113609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.087540 restraints weight = 25970.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.090392 restraints weight = 12629.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.092182 restraints weight = 7969.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8950  Z= 0.130
  Angle     :  0.640  12.536  12092  Z= 0.319
  Chirality :  0.041   0.152   1440
  Planarity :  0.003   0.030   1532
  Dihedral  :  4.447  17.137   1238
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 31.20 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1134
  helix:  1.27 (0.19), residues: 780
  sheet: -3.00 (0.99), residues: 24
  loop : -1.42 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  66 
 HIS   0.013   0.001   HIS A 214 
 PHE   0.036   0.002   PHE B 116 
 TYR   0.018   0.001   TYR B 130 
 ARG   0.011   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  544)
  hydrogen bonds       : angle       4.28958 ( 1614)
  covalent geometry    : bond        0.00309 ( 8950)
  covalent geometry    : angle       0.63971 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  402 MET cc_start: 0.7757 (mmm) cc_final: 0.7398 (mmm)
REVERT: B  410 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7261 (m-80)
REVERT: A  170 ILE cc_start: 0.9278 (tp) cc_final: 0.8896 (tp)
REVERT: A  324 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7744 (t)
REVERT: A  339 THR cc_start: 0.8495 (m) cc_final: 0.8118 (p)
REVERT: A  349 PHE cc_start: 0.7608 (t80) cc_final: 0.6707 (t80)
REVERT: A  456 MET cc_start: 0.8516 (mmm) cc_final: 0.8200 (mmm)
REVERT: A  480 LEU cc_start: 0.9061 (tp) cc_final: 0.8714 (tt)
REVERT: A  481 LEU cc_start: 0.8714 (mt) cc_final: 0.8502 (mt)
  outliers start: 35
  outliers final: 26
  residues processed: 160
  average time/residue: 0.1800
  time to fit residues: 42.2200
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  237 MET
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0270
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.2046

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
** A 485 GLN ** 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 = 0.3936 r_free = 0.3936 target = 0.115561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.089465 restraints weight = 26620.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.092233 restraints weight = 12985.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.093985 restraints weight = 8257.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   8950  Z= 0.157
  Angle     :  0.677  11.164  12092  Z= 0.336
  Chirality :  0.042   0.142   1440
  Planarity :  0.004   0.030   1532
  Dihedral  :  4.493  20.781   1238
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 32.75 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1134
  helix:  1.19 (0.19), residues: 780
  sheet: -3.07 (0.98), residues: 24
  loop : -1.44 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  66 
 HIS   0.011   0.001   HIS A 214 
 PHE   0.038   0.002   PHE B 115 
 TYR   0.017   0.001   TYR B 572 
 ARG   0.011   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  544)
  hydrogen bonds       : angle       4.38462 ( 1614)
  covalent geometry    : bond        0.00372 ( 8950)
  covalent geometry    : angle       0.67713 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  402 MET cc_start: 0.7807 (mmm) cc_final: 0.7539 (mmm)
REVERT: B  410 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7271 (m-80)
REVERT: A  170 ILE cc_start: 0.9294 (tp) cc_final: 0.8911 (tp)
REVERT: A  312 MET cc_start: 0.7069 (mmm) cc_final: 0.6586 (ttt)
REVERT: A  324 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7799 (t)
REVERT: A  339 THR cc_start: 0.8488 (m) cc_final: 0.8107 (p)
REVERT: A  402 MET cc_start: 0.7878 (mmm) cc_final: 0.7673 (mmm)
REVERT: A  456 MET cc_start: 0.8577 (mmm) cc_final: 0.8201 (mmm)
REVERT: A  480 LEU cc_start: 0.9099 (tp) cc_final: 0.8780 (tt)
REVERT: A  481 LEU cc_start: 0.8767 (mt) cc_final: 0.8535 (mt)
  outliers start: 35
  outliers final: 28
  residues processed: 146
  average time/residue: 0.1732
  time to fit residues: 37.0038
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 87 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
** A 485 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.114614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.088801 restraints weight = 26332.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.091638 restraints weight = 12843.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093513 restraints weight = 8113.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110   8950  Z= 0.134
  Angle     :  0.668  10.848  12092  Z= 0.330
  Chirality :  0.041   0.196   1440
  Planarity :  0.003   0.031   1532
  Dihedral  :  4.427  16.660   1238
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 33.16 %
    Favored  : 63.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1134
  helix:  1.19 (0.19), residues: 780
  sheet: -2.95 (1.00), residues: 24
  loop : -1.42 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  66 
 HIS   0.010   0.001   HIS A 214 
 PHE   0.033   0.001   PHE B 115 
 TYR   0.021   0.001   TYR B 130 
 ARG   0.011   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  544)
  hydrogen bonds       : angle       4.33372 ( 1614)
  covalent geometry    : bond        0.00315 ( 8950)
  covalent geometry    : angle       0.66836 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  410 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7168 (m-80)
REVERT: A   98 MET cc_start: 0.7854 (tmm) cc_final: 0.7348 (tmm)
REVERT: A  170 ILE cc_start: 0.9286 (tp) cc_final: 0.8904 (tp)
REVERT: A  312 MET cc_start: 0.7140 (mmm) cc_final: 0.6602 (ttt)
REVERT: A  324 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7687 (t)
REVERT: A  339 THR cc_start: 0.8480 (m) cc_final: 0.8102 (p)
REVERT: A  456 MET cc_start: 0.8440 (mmm) cc_final: 0.8199 (mmm)
REVERT: A  480 LEU cc_start: 0.9077 (tp) cc_final: 0.8740 (tt)
REVERT: A  481 LEU cc_start: 0.8740 (mt) cc_final: 0.8489 (mt)
  outliers start: 35
  outliers final: 27
  residues processed: 150
  average time/residue: 0.1791
  time to fit residues: 39.0212
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0270
   chunk 70 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0470
   chunk 15 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 88 optimal weight:   20.0000
   chunk 100 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
** A 485 GLN ** 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 = 0.3984 r_free = 0.3984 target = 0.116879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.090912 restraints weight = 26121.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093784 restraints weight = 12716.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.095641 restraints weight = 8000.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113   8950  Z= 0.125
  Angle     :  0.663  10.474  12092  Z= 0.327
  Chirality :  0.041   0.198   1440
  Planarity :  0.003   0.030   1532
  Dihedral  :  4.364  15.952   1238
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 33.68 %
    Favored  : 63.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1134
  helix:  1.20 (0.19), residues: 770
  sheet: -2.91 (0.99), residues: 24
  loop : -1.37 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  66 
 HIS   0.022   0.002   HIS A 214 
 PHE   0.032   0.002   PHE B 115 
 TYR   0.013   0.001   TYR B 572 
 ARG   0.010   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  544)
  hydrogen bonds       : angle       4.23840 ( 1614)
  covalent geometry    : bond        0.00292 ( 8950)
  covalent geometry    : angle       0.66342 (12092)

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

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: B  312 MET cc_start: 0.3356 (tpt) cc_final: 0.3064 (tpt)
REVERT: B  410 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7241 (m-80)
REVERT: B  460 MET cc_start: 0.8424 (ptp) cc_final: 0.8018 (pmm)
REVERT: A  170 ILE cc_start: 0.9281 (tp) cc_final: 0.8909 (tp)
REVERT: A  324 SER cc_start: 0.7953 (OUTLIER) cc_final: 0.7645 (t)
REVERT: A  339 THR cc_start: 0.8481 (m) cc_final: 0.8119 (p)
REVERT: A  456 MET cc_start: 0.8453 (mmm) cc_final: 0.8043 (tpt)
REVERT: A  480 LEU cc_start: 0.9084 (tp) cc_final: 0.8729 (tt)
REVERT: A  481 LEU cc_start: 0.8791 (mt) cc_final: 0.8493 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 148
  average time/residue: 0.1741
  time to fit residues: 37.8195
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   chunk 102 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 427 HIS
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 485 GLN ** 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 = 0.3974 r_free = 0.3974 target = 0.115475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.089722 restraints weight = 26466.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.092498 restraints weight = 13230.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.094275 restraints weight = 8480.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8950  Z= 0.141
  Angle     :  0.676  11.352  12092  Z= 0.333
  Chirality :  0.041   0.186   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  4.376  15.387   1238
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 33.99 %
    Favored  : 63.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1134
  helix:  1.19 (0.19), residues: 782
  sheet: -3.02 (0.97), residues: 24
  loop : -1.41 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  66 
 HIS   0.020   0.002   HIS A 214 
 PHE   0.040   0.002   PHE A 429 
 TYR   0.021   0.001   TYR B 130 
 ARG   0.016   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03667 (  544)
  hydrogen bonds       : angle       4.25032 ( 1614)
  covalent geometry    : bond        0.00337 ( 8950)
  covalent geometry    : angle       0.67650 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3238.49 seconds
wall clock time: 57 minutes 26.65 seconds (3446.65 seconds total)