Starting phenix.real_space_refine
on Sat Aug 23 00:58:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsq_41598/08_2025/8tsq_41598.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.052
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    5652      2.51       5
     N    1552      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4459
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4459
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
  Time building chain proxies: 1.73, per 1000 atoms: 0.19
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (75.615, 133.125, 135.255, 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    1660      8.00
     N    1552      7.00
     C    5652      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 231.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 4 sheets defined
      69.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.538A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 62 through 109
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 3.817A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 4.054A  pdb=" N   ASP A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   SER A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ALA A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 212
      Proline residue:  A 176  - end of helix
      removed outlier: 4.072A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 4.132A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 272
      removed outlier: 3.953A  pdb=" N   GLU A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.583A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 4.108A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 294
      removed outlier: 3.724A  pdb=" N   ILE A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 322
      removed outlier: 3.696A  pdb=" N   LYS A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 389
    Processing helix  chain 'A' and resid 415 through 417
      No H-bonds generated for 'chain 'A' and resid 415 through 417'
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 465
      removed outlier: 4.022A  pdb=" N   LYS A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.540A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 497
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.868A  pdb=" N   ILE A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'B' and resid 8 through 21
      removed outlier: 3.799A  pdb=" N   THR B  12 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 3.513A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.541A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP B  54 " --> pdb=" O   PRO B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.779A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 164
      removed outlier: 3.597A  pdb=" N   LEU B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ALA B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 212
      Proline residue:  B 176  - end of helix
      removed outlier: 4.102A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 4.130A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
      removed outlier: 3.970A  pdb=" N   GLU B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 272
      removed outlier: 3.906A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 277
      removed outlier: 4.046A  pdb=" N   ASP B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 294
      removed outlier: 3.760A  pdb=" N   ILE B 292 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 322
      removed outlier: 3.560A  pdb=" N   LYS B 299 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 389
    Processing helix  chain 'B' and resid 414 through 418
      removed outlier: 3.744A  pdb=" N   GLN B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 414 through 418'
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 4.036A  pdb=" N   LYS B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 515 through 527
      removed outlier: 3.853A  pdb=" N   ILE B 519 " --> pdb=" O   SER B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 366
      removed outlier: 5.628A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.449A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 366
      removed outlier: 6.474A  pdb=" N   ARG B 360 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   THR B 348 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   ILE B 362 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.218A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ASP B 505 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 505 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1668 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: 0.99

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2801
        1.34 -     1.46: 1173
        1.46 -     1.58: 4972
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" N   VAL B 113 "
       pdb=" CA  VAL B 113 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.24e-02 6.50e+03 6.93e+00
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.26e-02 6.30e+03 6.89e+00
  bond pdb=" N   MET A 109 "
       pdb=" CA  MET A 109 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.22e-02 6.72e+03 5.43e+00
  bond pdb=" N   MET A 111 "
       pdb=" CA  MET A 111 "
    ideal  model  delta    sigma   weight residual
    1.452  1.488 -0.035 1.54e-02 4.22e+03 5.29e+00
  bond pdb=" N   MET B 111 "
       pdb=" CA  MET B 111 "
    ideal  model  delta    sigma   weight residual
    1.451  1.488 -0.037 1.69e-02 3.50e+03 4.89e+00
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 12014
        2.01 -     4.01: 178
        4.01 -     6.02: 27
        6.02 -     8.03: 5
        8.03 -    10.03: 6
  Bond angle restraints: 12230
  Sorted by residual:
  angle pdb=" N   GLY B 110 "
        pdb=" CA  GLY B 110 "
        pdb=" C   GLY B 110 "
      ideal   model   delta    sigma   weight residual
     115.32  109.41    5.91 1.48e+00 4.57e-01 1.60e+01
  angle pdb=" N   GLY A 110 "
        pdb=" CA  GLY A 110 "
        pdb=" C   GLY A 110 "
      ideal   model   delta    sigma   weight residual
     115.32  110.13    5.19 1.48e+00 4.57e-01 1.23e+01
  angle pdb=" CA  MET A 109 "
        pdb=" C   MET A 109 "
        pdb=" O   MET A 109 "
      ideal   model   delta    sigma   weight residual
     121.16  117.74    3.42 1.12e+00 7.97e-01 9.30e+00
  angle pdb=" CB  MET B 200 "
        pdb=" CG  MET B 200 "
        pdb=" SD  MET B 200 "
      ideal   model   delta    sigma   weight residual
     112.70  121.38   -8.68 3.00e+00 1.11e-01 8.37e+00
  angle pdb=" CA  LEU A 294 "
        pdb=" CB  LEU A 294 "
        pdb=" CG  LEU A 294 "
      ideal   model   delta    sigma   weight residual
     116.30  126.33  -10.03 3.50e+00 8.16e-02 8.22e+00
  ... (remaining 12225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4777
       17.95 -    35.90: 545
       35.90 -    53.84: 133
       53.84 -    71.79: 41
       71.79 -    89.74: 8
  Dihedral angle restraints: 5504
    sinusoidal: 2182
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  ARG A 391 "
           pdb=" C   ARG A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.18   20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ARG B 391 "
           pdb=" C   ARG B 391 "
           pdb=" N   PHE B 392 "
           pdb=" CA  PHE B 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.25   20.75     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  ASP B 467 "
           pdb=" CB  ASP B 467 "
           pdb=" CG  ASP B 467 "
           pdb=" OD1 ASP B 467 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.42   59.42     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 5501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1037
       0.040 -    0.080: 319
       0.080 -    0.120: 90
       0.120 -    0.160: 5
       0.160 -    0.200: 3
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CA  MET A 109 "
            pdb=" N   MET A 109 "
            pdb=" C   MET A 109 "
            pdb=" CB  MET A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.98e-01
  chirality pdb=" CB  ILE B 258 "
            pdb=" CA  ILE B 258 "
            pdb=" CG1 ILE B 258 "
            pdb=" CG2 ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.92e-01
  chirality pdb=" CA  MET B 111 "
            pdb=" N   MET B 111 "
            pdb=" C   MET B 111 "
            pdb=" CB  MET B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.04e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 410 "   -0.017 2.00e-02 2.50e+03   1.15e-02 2.63e+00
        pdb=" CG  TYR B 410 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 410 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 410 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 410 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 410 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 410 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 410 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 109 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   MET B 109 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET B 109 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLY B 110 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 462 "    0.008 2.00e-02 2.50e+03   1.07e-02 2.00e+00
        pdb=" CG  PHE A 462 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 462 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 462 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 462 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 462 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 462 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1544
        2.77 -     3.30: 9259
        3.30 -     3.83: 14858
        3.83 -     4.37: 16240
        4.37 -     4.90: 28196
  Nonbonded interactions: 70097
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 357 "
            pdb=" NH2 ARG B 360 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OD1 ASN A 430 "
            pdb=" NE2 GLN B 209 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" NE2 GLN A 209 "
            pdb=" OD1 ASN B 430 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG1 THR A 561 "
            pdb=" OD1 ASN A 563 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG  SER B 446 "
            pdb=" OE1 GLN B 449 "
     model   vdw
     2.311 3.040
  ... (remaining 70092 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.940
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
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   0.047   9050  Z= 0.178
  Angle     :  0.655  10.034  12230  Z= 0.361
  Chirality :  0.041   0.200   1454
  Planarity :  0.004   0.045   1548
  Dihedral  : 16.891  89.739   3356
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 22.90 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.25), residues: 1146
  helix:  1.68 (0.19), residues: 720
  sheet:  0.31 (0.55), residues: 86
  loop : -1.40 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 559 
 TYR   0.026   0.002   TYR B 410 
 PHE   0.024   0.001   PHE A 462 
 TRP   0.011   0.001   TRP A  17 
 HIS   0.005   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9050)
  covalent geometry    : angle       0.65491 (12230)
  hydrogen bonds       : bond        0.14103 (  570)
  hydrogen bonds       : angle       4.81281 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7367 (ttm) cc_final: 0.7138 (ttm)
  outliers start: 5
  outliers final: 1
  residues processed: 119
  average time/residue: 0.0665
  time to fit residues: 11.5923
Evaluate side-chains
  111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  393 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 240 GLN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.4722 r_free = 0.4722 target = 0.253517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.235002 restraints weight = 8952.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.225939 restraints weight = 12372.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.223958 restraints weight = 16574.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.224222 restraints weight = 14400.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.224131 restraints weight = 12286.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9050  Z= 0.134
  Angle     :  0.539   8.407  12230  Z= 0.284
  Chirality :  0.040   0.137   1454
  Planarity :  0.004   0.035   1548
  Dihedral  :  4.338  42.358   1252
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.45 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.25), residues: 1146
  helix:  1.75 (0.19), residues: 738
  sheet:  0.24 (0.57), residues: 86
  loop : -1.55 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 559 
 TYR   0.016   0.001   TYR B 410 
 PHE   0.019   0.001   PHE B 189 
 TRP   0.009   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9050)
  covalent geometry    : angle       0.53902 (12230)
  hydrogen bonds       : bond        0.04909 (  570)
  hydrogen bonds       : angle       4.01754 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  312 MET cc_start: 0.7884 (mmp) cc_final: 0.7533 (mmp)
REVERT: B  312 MET cc_start: 0.7864 (mmp) cc_final: 0.7463 (mmp)
REVERT: B  346 ASN cc_start: 0.6045 (t0) cc_final: 0.5678 (t0)
REVERT: B  416 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8200 (mtt-85)
  outliers start: 33
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0572
  time to fit residues: 12.8193
Evaluate side-chains
  136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  410 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 101 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0000
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.253450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.234937 restraints weight = 8901.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.231307 restraints weight = 13415.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.229916 restraints weight = 14441.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.228774 restraints weight = 12945.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.228411 restraints weight = 11468.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.132
  Angle     :  0.524   8.617  12230  Z= 0.276
  Chirality :  0.040   0.148   1454
  Planarity :  0.004   0.036   1548
  Dihedral  :  4.296  46.381   1252
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.45 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.25), residues: 1146
  helix:  1.81 (0.19), residues: 750
  sheet:  0.03 (0.57), residues: 88
  loop : -1.73 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 559 
 TYR   0.019   0.001   TYR B 410 
 PHE   0.019   0.001   PHE B 462 
 TRP   0.008   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9050)
  covalent geometry    : angle       0.52403 (12230)
  hydrogen bonds       : bond        0.04807 (  570)
  hydrogen bonds       : angle       3.94750 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  312 MET cc_start: 0.8018 (mmp) cc_final: 0.7737 (mmp)
REVERT: B   75 MET cc_start: 0.6474 (mtp) cc_final: 0.6224 (mtp)
REVERT: B   98 MET cc_start: 0.7635 (ttp) cc_final: 0.7269 (ttm)
  outliers start: 34
  outliers final: 22
  residues processed: 144
  average time/residue: 0.0619
  time to fit residues: 13.2813
Evaluate side-chains
  137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 537 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.204749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.171566 restraints weight = 9703.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.169403 restraints weight = 18185.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.169624 restraints weight = 18222.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.169237 restraints weight = 12652.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.169476 restraints weight = 11962.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9050  Z= 0.132
  Angle     :  0.524   9.040  12230  Z= 0.274
  Chirality :  0.040   0.131   1454
  Planarity :  0.003   0.036   1548
  Dihedral  :  4.291  50.603   1252
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.04 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.25), residues: 1146
  helix:  1.86 (0.19), residues: 750
  sheet:  0.01 (0.57), residues: 88
  loop : -1.73 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 559 
 TYR   0.016   0.001   TYR B 410 
 PHE   0.021   0.001   PHE A 462 
 TRP   0.007   0.001   TRP B  17 
 HIS   0.006   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9050)
  covalent geometry    : angle       0.52380 (12230)
  hydrogen bonds       : bond        0.04759 (  570)
  hydrogen bonds       : angle       3.88980 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   98 MET cc_start: 0.7356 (ttp) cc_final: 0.7046 (ttm)
REVERT: A  312 MET cc_start: 0.7909 (mmp) cc_final: 0.7614 (mmp)
REVERT: A  382 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5545 (pptt)
REVERT: B  416 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8192 (mtt-85)
  outliers start: 39
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0593
  time to fit residues: 12.7894
Evaluate side-chains
  138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.257387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.234916 restraints weight = 9727.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.218453 restraints weight = 14268.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.215390 restraints weight = 12013.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.215894 restraints weight = 10963.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.216436 restraints weight = 9496.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9050  Z= 0.149
  Angle     :  0.548   9.184  12230  Z= 0.287
  Chirality :  0.041   0.134   1454
  Planarity :  0.004   0.045   1548
  Dihedral  :  4.371  54.520   1252
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.86 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.25), residues: 1146
  helix:  1.84 (0.19), residues: 750
  sheet:  0.00 (0.58), residues: 88
  loop : -1.75 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 559 
 TYR   0.015   0.002   TYR B 410 
 PHE   0.027   0.002   PHE B 462 
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9050)
  covalent geometry    : angle       0.54791 (12230)
  hydrogen bonds       : bond        0.04963 (  570)
  hydrogen bonds       : angle       3.94786 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  382 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5794 (pptt)
REVERT: B  346 ASN cc_start: 0.6871 (t0) cc_final: 0.6565 (t0)
REVERT: B  416 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8254 (mtt-85)
  outliers start: 36
  outliers final: 28
  residues processed: 142
  average time/residue: 0.0808
  time to fit residues: 17.0771
Evaluate side-chains
  143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  448 GLU
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 71 optimal weight:    0.2980
   chunk 98 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 HIS
B 198 ASN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 HIS
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.260517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.232642 restraints weight = 9435.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.219517 restraints weight = 12764.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.220496 restraints weight = 9035.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.220651 restraints weight = 7918.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.221122 restraints weight = 6852.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.121
  Angle     :  0.534  10.175  12230  Z= 0.274
  Chirality :  0.039   0.129   1454
  Planarity :  0.003   0.052   1548
  Dihedral  :  4.317  59.727   1252
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.06 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1146
  helix:  1.99 (0.19), residues: 750
  sheet:  0.01 (0.58), residues: 88
  loop : -1.68 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 559 
 TYR   0.015   0.001   TYR B 410 
 PHE   0.016   0.001   PHE B 189 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9050)
  covalent geometry    : angle       0.53442 (12230)
  hydrogen bonds       : bond        0.04543 (  570)
  hydrogen bonds       : angle       3.80927 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  111 MET cc_start: 0.7406 (ttm) cc_final: 0.7170 (ttt)
REVERT: A  346 ASN cc_start: 0.6938 (t0) cc_final: 0.6471 (t0)
REVERT: A  382 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5751 (pptt)
REVERT: B   44 MET cc_start: 0.7887 (ttp) cc_final: 0.7641 (ttt)
REVERT: B   75 MET cc_start: 0.6840 (mtp) cc_final: 0.6478 (mtp)
REVERT: B  312 MET cc_start: 0.7645 (mmp) cc_final: 0.7285 (mmp)
REVERT: B  346 ASN cc_start: 0.7018 (t0) cc_final: 0.6640 (t0)
  outliers start: 37
  outliers final: 28
  residues processed: 154
  average time/residue: 0.0799
  time to fit residues: 18.2966
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  448 GLU
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 113 optimal weight:   20.0000
   chunk 20 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 111 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
** B 418 GLN ** 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 = 0.4882 r_free = 0.4882 target = 0.256445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.227998 restraints weight = 9481.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.212278 restraints weight = 13050.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.213720 restraints weight = 9269.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.214048 restraints weight = 7429.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.214241 restraints weight = 7629.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.4486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9050  Z= 0.149
  Angle     :  0.567  10.844  12230  Z= 0.292
  Chirality :  0.041   0.137   1454
  Planarity :  0.004   0.054   1548
  Dihedral  :  4.373  55.763   1252
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.37 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.25), residues: 1146
  helix:  1.90 (0.19), residues: 750
  sheet: -0.08 (0.58), residues: 88
  loop : -1.72 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 559 
 TYR   0.015   0.002   TYR B 410 
 PHE   0.019   0.002   PHE A  56 
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9050)
  covalent geometry    : angle       0.56738 (12230)
  hydrogen bonds       : bond        0.04907 (  570)
  hydrogen bonds       : angle       3.91546 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  196 MET cc_start: 0.3245 (tpp) cc_final: 0.2902 (tpp)
REVERT: A  382 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.5829 (pptt)
REVERT: A  538 ARG cc_start: 0.7853 (ttm110) cc_final: 0.6923 (mpt180)
REVERT: B  346 ASN cc_start: 0.7052 (t0) cc_final: 0.6668 (t0)
REVERT: B  416 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8227 (mtt-85)
  outliers start: 39
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0940
  time to fit residues: 19.0148
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  448 GLU
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 88 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0050
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 ASN ** 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 = 0.4899 r_free = 0.4899 target = 0.258621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.229955 restraints weight = 9385.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.216049 restraints weight = 13667.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.218769 restraints weight = 9597.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.218838 restraints weight = 7867.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.219440 restraints weight = 6984.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.4519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9050  Z= 0.132
  Angle     :  0.564  10.784  12230  Z= 0.288
  Chirality :  0.040   0.134   1454
  Planarity :  0.004   0.061   1548
  Dihedral  :  4.308  50.863   1252
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.88 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1146
  helix:  1.98 (0.19), residues: 750
  sheet: -0.04 (0.58), residues: 88
  loop : -1.63 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 559 
 TYR   0.017   0.001   TYR B 410 
 PHE   0.016   0.001   PHE B 189 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9050)
  covalent geometry    : angle       0.56365 (12230)
  hydrogen bonds       : bond        0.04673 (  570)
  hydrogen bonds       : angle       3.81820 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  260 SER cc_start: 0.8697 (t) cc_final: 0.8383 (t)
REVERT: A  310 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6861 (tmm-80)
REVERT: A  382 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5797 (pptt)
REVERT: A  538 ARG cc_start: 0.7765 (ttm110) cc_final: 0.6887 (mpt180)
REVERT: B  310 ARG cc_start: 0.6974 (tmm-80) cc_final: 0.6696 (tmm-80)
REVERT: B  346 ASN cc_start: 0.6999 (t0) cc_final: 0.6613 (t0)
REVERT: B  393 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7614 (p90)
REVERT: B  416 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8227 (mtt-85)
  outliers start: 34
  outliers final: 28
  residues processed: 143
  average time/residue: 0.0831
  time to fit residues: 16.6323
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    0.0570
   chunk 36 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 106 optimal weight:    0.0010
   chunk 65 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 113 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.4904

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 ASN ** 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 = 0.4899 r_free = 0.4899 target = 0.267596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.236072 restraints weight = 9940.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.217568 restraints weight = 13507.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.218995 restraints weight = 11100.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.221597 restraints weight = 8718.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.221724 restraints weight = 7108.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9050  Z= 0.125
  Angle     :  0.563  10.926  12230  Z= 0.286
  Chirality :  0.040   0.144   1454
  Planarity :  0.004   0.058   1548
  Dihedral  :  4.235  47.368   1252
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.47 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.26), residues: 1146
  helix:  2.16 (0.19), residues: 736
  sheet: -0.04 (0.58), residues: 88
  loop : -1.49 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 559 
 TYR   0.020   0.001   TYR B 410 
 PHE   0.017   0.001   PHE B 462 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9050)
  covalent geometry    : angle       0.56340 (12230)
  hydrogen bonds       : bond        0.04452 (  570)
  hydrogen bonds       : angle       3.74410 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  310 ARG cc_start: 0.7147 (tmm-80) cc_final: 0.6890 (tmm-80)
REVERT: A  382 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5838 (pptt)
REVERT: A  538 ARG cc_start: 0.7864 (ttm110) cc_final: 0.6808 (mmt-90)
REVERT: B   75 MET cc_start: 0.6687 (mtp) cc_final: 0.6317 (mtp)
REVERT: B  310 ARG cc_start: 0.7068 (tmm-80) cc_final: 0.6754 (tmm-80)
REVERT: B  346 ASN cc_start: 0.7332 (t0) cc_final: 0.6931 (t0)
REVERT: B  393 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7752 (p90)
REVERT: B  416 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8059 (mtt-85)
  outliers start: 37
  outliers final: 30
  residues processed: 147
  average time/residue: 0.0761
  time to fit residues: 15.9487
Evaluate side-chains
  150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.4873 r_free = 0.4873 target = 0.264218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.232195 restraints weight = 9829.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.212655 restraints weight = 14193.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.215233 restraints weight = 10175.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.214847 restraints weight = 8941.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.215145 restraints weight = 7940.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9050  Z= 0.156
  Angle     :  0.623  11.423  12230  Z= 0.314
  Chirality :  0.041   0.164   1454
  Planarity :  0.004   0.055   1548
  Dihedral  :  4.363  43.194   1252
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.96 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1146
  helix:  1.98 (0.19), residues: 738
  sheet: -0.06 (0.58), residues: 88
  loop : -1.54 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 559 
 TYR   0.026   0.002   TYR B 410 
 PHE   0.017   0.002   PHE B 189 
 TRP   0.007   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9050)
  covalent geometry    : angle       0.62291 (12230)
  hydrogen bonds       : bond        0.04998 (  570)
  hydrogen bonds       : angle       3.93526 ( 1668)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  310 ARG cc_start: 0.7076 (tmm-80) cc_final: 0.6810 (tmm-80)
REVERT: A  382 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.5986 (pptt)
REVERT: A  538 ARG cc_start: 0.7886 (ttm110) cc_final: 0.6779 (mmt-90)
REVERT: B   44 MET cc_start: 0.8078 (ttm) cc_final: 0.7795 (ttm)
REVERT: B   75 MET cc_start: 0.6663 (mtp) cc_final: 0.6314 (mtp)
REVERT: B  310 ARG cc_start: 0.7063 (tmm-80) cc_final: 0.6437 (tmm-80)
REVERT: B  322 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7580 (tt)
REVERT: B  346 ASN cc_start: 0.7509 (t0) cc_final: 0.7079 (t0)
REVERT: B  393 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7617 (p90)
  outliers start: 37
  outliers final: 28
  residues processed: 145
  average time/residue: 0.0768
  time to fit residues: 15.8338
Evaluate side-chains
  148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  470 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  504 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 109 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 113 optimal weight:    8.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
A 520 GLN
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.267609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.237638 restraints weight = 9858.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.220669 restraints weight = 14667.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.219904 restraints weight = 12027.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.219780 restraints weight = 11668.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.220468 restraints weight = 9082.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9050  Z= 0.134
  Angle     :  0.586  10.713  12230  Z= 0.297
  Chirality :  0.040   0.149   1454
  Planarity :  0.004   0.062   1548
  Dihedral  :  4.314  42.328   1252
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.96 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.26), residues: 1146
  helix:  2.05 (0.19), residues: 738
  sheet: -0.03 (0.58), residues: 88
  loop : -1.51 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 559 
 TYR   0.028   0.001   TYR B 410 
 PHE   0.017   0.001   PHE B 189 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.000   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9050)
  covalent geometry    : angle       0.58637 (12230)
  hydrogen bonds       : bond        0.04664 (  570)
  hydrogen bonds       : angle       3.81875 ( 1668)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1438.78 seconds
wall clock time: 25 minutes 32.18 seconds (1532.18 seconds total)