Starting phenix.real_space_refine
on Thu Feb 13 09:27:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsq_41598/02_2025/8tsq_41598.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsq_41598/02_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_41598/02_2025/8tsq_41598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsq_41598/02_2025/8tsq_41598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsq_41598/02_2025/8tsq_41598.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsq_41598/02_2025/8tsq_41598.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.90, per 1000 atoms: 0.66
  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.95
  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: 2.64

  Time building geometry restraints manager: 2.61 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.400
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.920
-------------------------------------------------------------------------------
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= 0.238
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (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
 TRP   0.011   0.001   TRP A  17 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.024   0.001   PHE A 462 
 TYR   0.026   0.002   TYR B 410 
 ARG   0.014   0.000   ARG B 559 

*********************** 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  : 0.959 
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: 0.1953
  time to fit residues: 33.6227
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  : 1.044 
-------------------------------------------------------------------------------
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 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.1980
   chunk 89 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0980
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4731 r_free = 0.4731 target = 0.254688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.235600 restraints weight = 8862.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.221967 restraints weight = 13915.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.219086 restraints weight = 15950.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9050  Z= 0.173
  Angle     :  0.531   8.432  12230  Z= 0.279
  Chirality :  0.040   0.135   1454
  Planarity :  0.004   0.035   1548
  Dihedral  :  4.317  42.281   1252
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.94 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1146
  helix:  1.79 (0.19), residues: 738
  sheet:  0.24 (0.56), residues: 86
  loop : -1.53 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.018   0.001   PHE B 189 
 TYR   0.016   0.001   TYR B 410 
 ARG   0.008   0.000   ARG B 559 

*********************** 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
  159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  312 MET cc_start: 0.7832 (mmp) cc_final: 0.7482 (mmp)
REVERT: B  312 MET cc_start: 0.7840 (mmp) cc_final: 0.7451 (mmp)
REVERT: B  416 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8188 (mtt-85)
  outliers start: 33
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1758
  time to fit residues: 38.3979
Evaluate side-chains
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
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  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 2 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 47 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4709 r_free = 0.4709 target = 0.252453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.233134 restraints weight = 8983.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.221010 restraints weight = 13447.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.218319 restraints weight = 15942.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9050  Z= 0.200
  Angle     :  0.535   8.791  12230  Z= 0.281
  Chirality :  0.040   0.147   1454
  Planarity :  0.004   0.036   1548
  Dihedral  :  4.325  46.275   1252
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.14 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1146
  helix:  1.80 (0.19), residues: 750
  sheet:  0.02 (0.57), residues: 88
  loop : -1.70 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.018   0.002   PHE B 462 
 TYR   0.017   0.001   TYR B 410 
 ARG   0.009   0.000   ARG B 559 

*********************** 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
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7209 (ttt) cc_final: 0.6779 (ttp)
REVERT: A  312 MET cc_start: 0.7996 (mmp) cc_final: 0.7688 (mmp)
REVERT: B   75 MET cc_start: 0.6466 (mtp) cc_final: 0.6225 (mtp)
REVERT: B   98 MET cc_start: 0.7530 (ttp) cc_final: 0.7181 (ttm)
REVERT: B  346 ASN cc_start: 0.6146 (t0) cc_final: 0.5908 (t0)
  outliers start: 33
  outliers final: 23
  residues processed: 139
  average time/residue: 0.1814
  time to fit residues: 37.0182
Evaluate side-chains
  138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
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  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  410 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 49 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0270
   chunk 91 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 101 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 111 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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**
B 537 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.205509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.177441 restraints weight = 9517.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.175005 restraints weight = 16645.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.174306 restraints weight = 18181.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.1464

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= 0.196
  Angle     :  0.522   8.951  12230  Z= 0.274
  Chirality :  0.040   0.131   1454
  Planarity :  0.003   0.036   1548
  Dihedral  :  4.329  52.246   1252
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.25), residues: 1146
  helix:  1.87 (0.19), residues: 750
  sheet: -0.02 (0.57), residues: 88
  loop : -1.69 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.007   0.001   HIS B 537 
 PHE   0.027   0.002   PHE B 462 
 TYR   0.015   0.001   TYR B 410 
 ARG   0.009   0.000   ARG B 559 

*********************** 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
  157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 115
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A   98 MET cc_start: 0.7374 (ttp) cc_final: 0.7053 (ttm)
REVERT: A  312 MET cc_start: 0.7959 (mmp) cc_final: 0.7699 (mmp)
REVERT: A  382 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5433 (pptt)
REVERT: B  416 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8230 (mtt-85)
  outliers start: 42
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1877
  time to fit residues: 39.8262
Evaluate side-chains
  140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
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  168 SER
Chi-restraints excluded: chain A residue  257 LEU
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  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  448 GLU
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 26 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0870
   overall best weight:    0.8962

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.255832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.227934 restraints weight = 9337.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.212265 restraints weight = 12779.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.213261 restraints weight = 11597.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9050  Z= 0.233
  Angle     :  0.563  10.576  12230  Z= 0.293
  Chirality :  0.041   0.136   1454
  Planarity :  0.003   0.037   1548
  Dihedral  :  4.443  56.063   1252
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.25), residues: 1146
  helix:  1.82 (0.19), residues: 750
  sheet: -0.06 (0.58), residues: 88
  loop : -1.69 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 405 
 PHE   0.017   0.002   PHE B 189 
 TYR   0.016   0.002   TYR B 410 
 ARG   0.005   0.000   ARG B 559 

*********************** 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
  157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  111 MET cc_start: 0.6672 (ttt) cc_final: 0.6244 (ttp)
REVERT: A  346 ASN cc_start: 0.6663 (t0) cc_final: 0.6226 (t0)
REVERT: A  382 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.5802 (pptt)
REVERT: A  405 HIS cc_start: 0.7643 (m170) cc_final: 0.7349 (m170)
REVERT: B  416 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8259 (mtt-85)
  outliers start: 37
  outliers final: 29
  residues processed: 148
  average time/residue: 0.1837
  time to fit residues: 39.9923
Evaluate side-chains
  147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  168 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  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  124 LEU
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 111 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0670
   chunk 24 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 198 ASN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.258688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.230248 restraints weight = 9374.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.215559 restraints weight = 12482.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.218420 restraints weight = 9286.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.1778

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= 0.180
  Angle     :  0.537   9.956  12230  Z= 0.277
  Chirality :  0.040   0.135   1454
  Planarity :  0.004   0.046   1548
  Dihedral  :  4.362  58.647   1252
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.65 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1146
  helix:  1.97 (0.19), residues: 750
  sheet: -0.06 (0.58), residues: 88
  loop : -1.63 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.016   0.001   PHE B 189 
 TYR   0.016   0.001   TYR B 410 
 ARG   0.011   0.000   ARG B 559 

*********************** 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
  156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A  111 MET cc_start: 0.6766 (ttt) cc_final: 0.6535 (ttp)
REVERT: A  312 MET cc_start: 0.7606 (mmp) cc_final: 0.7341 (mmp)
REVERT: A  346 ASN cc_start: 0.6888 (t0) cc_final: 0.6557 (t0)
REVERT: A  382 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.5806 (pptt)
REVERT: B  312 MET cc_start: 0.7695 (mmp) cc_final: 0.7301 (mmp)
  outliers start: 37
  outliers final: 30
  residues processed: 145
  average time/residue: 0.1854
  time to fit residues: 39.8954
Evaluate side-chains
  147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
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   36 LEU
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  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 25 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.256302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.228251 restraints weight = 9441.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.212082 restraints weight = 13276.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.214106 restraints weight = 9370.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.4476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9050  Z= 0.219
  Angle     :  0.572  10.264  12230  Z= 0.292
  Chirality :  0.040   0.145   1454
  Planarity :  0.004   0.053   1548
  Dihedral  :  4.377  53.873   1252
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 21.27 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.26), residues: 1146
  helix:  1.91 (0.19), residues: 750
  sheet: -0.13 (0.58), residues: 88
  loop : -1.63 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 537 
 PHE   0.026   0.001   PHE A 115 
 TYR   0.016   0.001   TYR B 410 
 ARG   0.012   0.000   ARG B 559 

*********************** 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
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  312 MET cc_start: 0.7721 (mmp) cc_final: 0.7343 (mmp)
REVERT: A  346 ASN cc_start: 0.6943 (t0) cc_final: 0.6571 (t0)
REVERT: A  382 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.5832 (pptt)
REVERT: B  460 MET cc_start: 0.5931 (mmm) cc_final: 0.5179 (mmt)
  outliers start: 38
  outliers final: 30
  residues processed: 142
  average time/residue: 0.1865
  time to fit residues: 38.2654
Evaluate side-chains
  144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  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  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  257 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  317 THR
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  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 106 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 63 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.263309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.230918 restraints weight = 10038.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.210154 restraints weight = 15097.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 80)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.210079 restraints weight = 13272.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9050  Z= 0.230
  Angle     :  0.589  11.364  12230  Z= 0.300
  Chirality :  0.041   0.129   1454
  Planarity :  0.004   0.041   1548
  Dihedral  :  4.386  48.299   1252
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 21.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.26), residues: 1146
  helix:  1.87 (0.19), residues: 750
  sheet: -0.15 (0.58), residues: 88
  loop : -1.59 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.022   0.002   PHE B 462 
 TYR   0.018   0.002   TYR B 410 
 ARG   0.011   0.000   ARG B 559 

*********************** 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
  150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A  312 MET cc_start: 0.7783 (mmp) cc_final: 0.7403 (mmp)
REVERT: A  346 ASN cc_start: 0.6897 (t0) cc_final: 0.6488 (t0)
REVERT: A  382 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6011 (pptt)
REVERT: A  538 ARG cc_start: 0.7821 (ttm110) cc_final: 0.6863 (mmt-90)
REVERT: B  310 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6815 (tmm-80)
REVERT: B  393 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7493 (p90)
  outliers start: 35
  outliers final: 30
  residues processed: 139
  average time/residue: 0.1998
  time to fit residues: 39.8576
Evaluate side-chains
  144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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  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  128 ILE
Chi-restraints excluded: chain B residue  164 SER
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  284 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 113 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.262938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.232479 restraints weight = 9908.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 80)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.208875 restraints weight = 15127.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.210358 restraints weight = 13517.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9050  Z= 0.242
  Angle     :  0.614  11.141  12230  Z= 0.312
  Chirality :  0.041   0.134   1454
  Planarity :  0.003   0.037   1548
  Dihedral  :  4.412  45.299   1252
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.57 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.26), residues: 1146
  helix:  1.92 (0.19), residues: 738
  sheet: -0.23 (0.57), residues: 88
  loop : -1.48 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.018   0.002   PHE A 115 
 TYR   0.026   0.002   TYR B 410 
 ARG   0.008   0.000   ARG B 559 

*********************** 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
  155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  310 ARG cc_start: 0.7164 (tmm-80) cc_final: 0.6908 (tmm-80)
REVERT: A  312 MET cc_start: 0.7749 (mmp) cc_final: 0.7355 (mmp)
REVERT: A  346 ASN cc_start: 0.7134 (t0) cc_final: 0.6535 (t0)
REVERT: A  382 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6051 (pptt)
REVERT: A  538 ARG cc_start: 0.7838 (ttm110) cc_final: 0.6792 (mmt-90)
REVERT: B  310 ARG cc_start: 0.7093 (tmm-80) cc_final: 0.6422 (tmm-80)
REVERT: B  393 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7519 (p90)
REVERT: B  460 MET cc_start: 0.6020 (mmm) cc_final: 0.5191 (mmt)
  outliers start: 39
  outliers final: 31
  residues processed: 143
  average time/residue: 0.2023
  time to fit residues: 40.8231
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
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  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  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  128 ILE
Chi-restraints excluded: chain B residue  164 SER
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  284 ILE
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 66 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 197 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 ** 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 = 0.4878 r_free = 0.4878 target = 0.265615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.233773 restraints weight = 9984.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.214839 restraints weight = 14407.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.216405 restraints weight = 10530.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2124

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= 0.205
  Angle     :  0.593  11.155  12230  Z= 0.302
  Chirality :  0.040   0.131   1454
  Planarity :  0.004   0.050   1548
  Dihedral  :  4.347  41.759   1252
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1146
  helix:  2.02 (0.19), residues: 738
  sheet: -0.14 (0.61), residues: 80
  loop : -1.35 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.018   0.001   PHE A 115 
 TYR   0.032   0.001   TYR B 410 
 ARG   0.015   0.000   ARG B 559 

********************** 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
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  310 ARG cc_start: 0.7122 (tmm-80) cc_final: 0.6857 (tmm-80)
REVERT: A  312 MET cc_start: 0.7720 (mmp) cc_final: 0.7400 (mmp)
REVERT: A  346 ASN cc_start: 0.7128 (t0) cc_final: 0.6547 (t0)
REVERT: A  382 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6027 (pptt)
REVERT: A  538 ARG cc_start: 0.7849 (ttm110) cc_final: 0.6787 (mmt-90)
REVERT: B  310 ARG cc_start: 0.7069 (tmm-80) cc_final: 0.6777 (tmm-80)
REVERT: B  393 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7704 (p90)
REVERT: B  538 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7023 (mpt180)
  outliers start: 29
  outliers final: 26
  residues processed: 136
  average time/residue: 0.2185
  time to fit residues: 41.6095
Evaluate side-chains
  142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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  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   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  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  284 ILE
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 58 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 83 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN
B 405 HIS
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.266042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.236070 restraints weight = 9944.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.215130 restraints weight = 14648.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.216295 restraints weight = 11135.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2208

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= 0.204
  Angle     :  0.593  11.057  12230  Z= 0.301
  Chirality :  0.040   0.128   1454
  Planarity :  0.004   0.055   1548
  Dihedral  :  4.324  41.471   1252
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.98 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1146
  helix:  2.00 (0.19), residues: 738
  sheet: -0.16 (0.60), residues: 82
  loop : -1.37 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  17 
 HIS   0.003   0.000   HIS B 405 
 PHE   0.018   0.001   PHE A 115 
 TYR   0.031   0.001   TYR B 410 
 ARG   0.015   0.000   ARG B 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2852.58 seconds
wall clock time: 52 minutes 0.89 seconds (3120.89 seconds total)