Starting phenix.real_space_refine
on Mon Jul 28 03:01:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yas_39106/07_2025/8yas_39106.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.050
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: 8
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     Be      1      3.05       5
     C    6323      2.51       5
     N    1693      2.21       5
     O    1825      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9894
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 765, 6107
          Classifications: {'peptide': 765}
          Link IDs: {'PTRANS': 15, 'TRANS': 749}
    Chain: "Y"
      Number of atoms: 3275
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3275
          Classifications: {'peptide': 420}
          Link IDs: {'PTRANS': 20, 'TRANS': 399}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 480
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 1, 'TRANS': 56}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.12, per 1000 atoms: 0.62
  Number of scatterers: 9894
  At special positions: 0
  Unit cell: (93.74, 113.36, 116.63, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      46     16.00
     P       2     15.00
     Mg      1     11.99
     F       3      9.00
     O    1825      8.00
     N    1693      7.00
     C    6323      6.00
     Be      1      4.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.70
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2310

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      66.7% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 33
      removed outlier: 4.033A  pdb=" N   ARG A  18 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 55
      removed outlier: 4.270A  pdb=" N   ILE A  46 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY A  55 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 77
    Processing helix  chain 'A' and resid 82 through 94
    Processing helix  chain 'A' and resid 105 through 118
      removed outlier: 3.540A  pdb=" N   THR A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      Proline residue:  A 113  - end of helix
    Processing helix  chain 'A' and resid 130 through 149
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 177 through 188
      removed outlier: 3.536A  pdb=" N   ASN A 188 " --> pdb=" O   TYR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 196
    Processing helix  chain 'A' and resid 208 through 214
    Processing helix  chain 'A' and resid 215 through 218
    Processing helix  chain 'A' and resid 231 through 242
    Processing helix  chain 'A' and resid 262 through 273
    Processing helix  chain 'A' and resid 283 through 299
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 374 through 376
      No H-bonds generated for 'chain 'A' and resid 374 through 376'
    Processing helix  chain 'A' and resid 377 through 384
    Processing helix  chain 'A' and resid 410 through 427
    Processing helix  chain 'A' and resid 438 through 451
      removed outlier: 3.595A  pdb=" N   SER A 442 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN A 451 " --> pdb=" O   LYS A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 465
      No H-bonds generated for 'chain 'A' and resid 463 through 465'
    Processing helix  chain 'A' and resid 466 through 474
      removed outlier: 3.659A  pdb=" N   GLU A 472 " --> pdb=" O   ALA A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 515 through 528
      removed outlier: 3.776A  pdb=" N   ASP A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 550
    Processing helix  chain 'A' and resid 553 through 557
      removed outlier: 3.625A  pdb=" N   MET A 557 " --> pdb=" O   THR A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 619
      removed outlier: 3.851A  pdb=" N   ARG A 576 " --> pdb=" O   LYS A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 642
      removed outlier: 3.640A  pdb=" N   TYR A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 3.579A  pdb=" N   LEU A 657 " --> pdb=" O   LYS A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 676
    Processing helix  chain 'A' and resid 680 through 704
      removed outlier: 3.646A  pdb=" N   GLY A 704 " --> pdb=" O   GLU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 742
      removed outlier: 3.665A  pdb=" N   ARG A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   HIS A 739 " --> pdb=" O   ARG A 735 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 745
      No H-bonds generated for 'chain 'A' and resid 743 through 745'
    Processing helix  chain 'A' and resid 747 through 777
    Processing helix  chain 'Y' and resid 3 through 9
      removed outlier: 3.604A  pdb=" N   MET Y   9 " --> pdb=" O   ILE Y   5 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 11 through 33
    Processing helix  chain 'Y' and resid 40 through 47
      removed outlier: 3.928A  pdb=" N   LEU Y  44 " --> pdb=" O   ASN Y  40 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 74 through 89
      removed outlier: 3.920A  pdb=" N   MET Y  89 " --> pdb=" O   GLN Y  85 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 92 through 102
      removed outlier: 4.156A  pdb=" N   GLY Y 102 " --> pdb=" O   TRP Y  98 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 104 through 137
    Processing helix  chain 'Y' and resid 145 through 173
    Processing helix  chain 'Y' and resid 177 through 202
      removed outlier: 3.688A  pdb=" N   ILE Y 181 " --> pdb=" O   ASN Y 177 " (cutoff:3.500A)
      Proline residue:  Y 192  - end of helix
    Processing helix  chain 'Y' and resid 213 through 236
    Processing helix  chain 'Y' and resid 271 through 290
      removed outlier: 3.705A  pdb=" N   ILE Y 275 " --> pdb=" O   VAL Y 271 " (cutoff:3.500A)
      Proline residue:  Y 284  - end of helix
    Processing helix  chain 'Y' and resid 294 through 304
      removed outlier: 3.696A  pdb=" N   LEU Y 298 " --> pdb=" O   ASN Y 294 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 308 through 331
    Processing helix  chain 'Y' and resid 332 through 344
    Processing helix  chain 'Y' and resid 353 through 388
      removed outlier: 3.912A  pdb=" N   GLN Y 357 " --> pdb=" O   GLY Y 353 " (cutoff:3.500A)
      Proline residue:  Y 382  - end of helix
    Processing helix  chain 'Y' and resid 399 through 421
      removed outlier: 3.982A  pdb=" N   LEU Y 403 " --> pdb=" O   GLY Y 399 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 422 through 424
      No H-bonds generated for 'chain 'Y' and resid 422 through 424'
    Processing helix  chain 'E' and resid 3 through 16
      removed outlier: 3.643A  pdb=" N   LYS E  16 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 154
      removed outlier: 6.353A  pdb=" N   ALA A 204 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   MET A 370 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A 206 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 226
      removed outlier: 6.791A  pdb=" N   LEU A 221 " --> pdb=" O   THR A 354 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   THR A 354 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE A 223 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 253
      removed outlier: 3.527A  pdb=" N   ALA A 258 " --> pdb=" O   ASP A 253 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 309
      removed outlier: 3.955A  pdb=" N   ILE A 315 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402
    Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.426A  pdb=" N   LEU A 433 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A 432 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   ALA A 483 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   VAL A 434 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN A 457 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 57 through 60
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 238 through 242
    Processing sheet with id=AA9, first strand: chain 'Y' and resid 244 through 245

    632 hydrogen bonds defined for protein.
    1860 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: 3.07

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2140
        1.32 -     1.44: 2147
        1.44 -     1.56: 5680
        1.56 -     1.68: 3
        1.68 -     1.80: 94
  Bond restraints: 10064
  Sorted by residual:
  bond pdb=" F3  BEF A1002 "
       pdb="BE   BEF A1002 "
    ideal  model  delta    sigma   weight residual
    1.476  1.762 -0.286 2.00e-02 2.50e+03 2.05e+02
  bond pdb=" F2  BEF A1002 "
       pdb="BE   BEF A1002 "
    ideal  model  delta    sigma   weight residual
    1.476  1.761 -0.285 2.00e-02 2.50e+03 2.02e+02
  bond pdb=" F1  BEF A1002 "
       pdb="BE   BEF A1002 "
    ideal  model  delta    sigma   weight residual
    1.476  1.751 -0.275 2.00e-02 2.50e+03 1.88e+02
  bond pdb=" CG1 ILE A 764 "
       pdb=" CD1 ILE A 764 "
    ideal  model  delta    sigma   weight residual
    1.513  1.364  0.149 3.90e-02 6.57e+02 1.47e+01
  bond pdb=" CB  VAL A  69 "
       pdb=" CG2 VAL A  69 "
    ideal  model  delta    sigma   weight residual
    1.521  1.416  0.105 3.30e-02 9.18e+02 1.01e+01
  ... (remaining 10059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 13121
        2.69 -     5.38: 418
        5.38 -     8.07: 45
        8.07 -    10.76: 9
       10.76 -    13.44: 1
  Bond angle restraints: 13594
  Sorted by residual:
  angle pdb=" N   VAL A 399 "
        pdb=" CA  VAL A 399 "
        pdb=" C   VAL A 399 "
      ideal   model   delta    sigma   weight residual
     112.29  106.63    5.66 9.40e-01 1.13e+00 3.62e+01
  angle pdb=" C   ASP A  38 "
        pdb=" N   ASP A  39 "
        pdb=" CA  ASP A  39 "
      ideal   model   delta    sigma   weight residual
     121.54  131.11   -9.57 1.91e+00 2.74e-01 2.51e+01
  angle pdb=" CA  GLN A 529 "
        pdb=" CB  GLN A 529 "
        pdb=" CG  GLN A 529 "
      ideal   model   delta    sigma   weight residual
     114.10  123.40   -9.30 2.00e+00 2.50e-01 2.16e+01
  angle pdb=" C   THR A 394 "
        pdb=" N   ASN A 395 "
        pdb=" CA  ASN A 395 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.83e+01
  angle pdb=" CA  THR A 643 "
        pdb=" C   THR A 643 "
        pdb=" N   PRO A 644 "
      ideal   model   delta    sigma   weight residual
     118.16  121.05   -2.89 7.00e-01 2.04e+00 1.71e+01
  ... (remaining 13589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.23: 5612
       24.23 -    48.46: 390
       48.46 -    72.69: 69
       72.69 -    96.92: 4
       96.92 -   121.16: 1
  Dihedral angle restraints: 6076
    sinusoidal: 2485
      harmonic: 3591
  Sorted by residual:
  dihedral pdb=" O2A ADP A1003 "
           pdb=" O3A ADP A1003 "
           pdb=" PA  ADP A1003 "
           pdb=" PB  ADP A1003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   61.16 -121.16     1      2.00e+01 2.50e-03 3.64e+01
  dihedral pdb=" CA  ASP A 667 "
           pdb=" C   ASP A 667 "
           pdb=" N   GLU A 668 "
           pdb=" CA  GLU A 668 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.23   29.77     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  ASN A 451 "
           pdb=" C   ASN A 451 "
           pdb=" N   LYS A 452 "
           pdb=" CA  LYS A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 6073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 887
       0.056 -    0.113: 506
       0.113 -    0.169: 131
       0.169 -    0.225: 24
       0.225 -    0.281: 7
  Chirality restraints: 1555
  Sorted by residual:
  chirality pdb=" CB  VAL A 127 "
            pdb=" CA  VAL A 127 "
            pdb=" CG1 VAL A 127 "
            pdb=" CG2 VAL A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CB  ILE Y 397 "
            pdb=" CA  ILE Y 397 "
            pdb=" CG1 ILE Y 397 "
            pdb=" CG2 ILE Y 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CB  VAL A 307 "
            pdb=" CA  VAL A 307 "
            pdb=" CG1 VAL A 307 "
            pdb=" CG2 VAL A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 1552 not shown)

  Planarity restraints: 1740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL Y  36 "   -0.060 5.00e-02 4.00e+02   9.04e-02 1.31e+01
        pdb=" N   PRO Y  37 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  37 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  37 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A  32 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.98e+00
        pdb=" CG  ASP A  32 "   -0.049 2.00e-02 2.50e+03
        pdb=" OD1 ASP A  32 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP A  32 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 365 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   GLU A 365 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLU A 365 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LYS A 366 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1737 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 68
        2.51 -     3.11: 7195
        3.11 -     3.71: 15143
        3.71 -     4.30: 22037
        4.30 -     4.90: 37202
  Nonbonded interactions: 81645
  Sorted by model distance:
  nonbonded pdb="MG    MG A1001 "
            pdb=" F3  BEF A1002 "
     model   vdw
     1.919 2.120
  nonbonded pdb="MG    MG A1001 "
            pdb=" O1B ADP A1003 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" F3  BEF A1002 "
            pdb=" O1B ADP A1003 "
     model   vdw
     2.164 2.990
  nonbonded pdb=" CD1 LEU A 740 "
            pdb=" OH  TYR Y 245 "
     model   vdw
     2.196 3.460
  nonbonded pdb=" CD1 PHE A 757 "
            pdb=" CE1 TYR Y 425 "
     model   vdw
     2.202 3.640
  ... (remaining 81640 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             6.000
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.160
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
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      :  0.020   0.900  10065  Z= 1.164
  Angle     :  1.107  13.444  13594  Z= 0.611
  Chirality :  0.071   0.281   1555
  Planarity :  0.008   0.090   1740
  Dihedral  : 16.480 121.156   3766
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 16.02 %
    Favored  : 83.32 %
  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: -3.32 (0.19), residues: 1235
  helix: -1.97 (0.14), residues: 786
  sheet: -1.32 (0.55), residues: 81
  loop : -2.51 (0.27), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP Y 165 
 HIS   0.006   0.002   HIS A  93 
 PHE   0.023   0.004   PHE A 703 
 TYR   0.027   0.004   TYR Y 306 
 ARG   0.005   0.001   ARG A  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14450 (  630)
  hydrogen bonds       : angle       6.43374 ( 1860)
  covalent geometry    : bond        0.01774 (10064)
  covalent geometry    : angle       1.10693 (13594)
  Misc. bond           : bond        0.89972 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 409
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 THR cc_start: 0.8701 (p) cc_final: 0.8414 (t)
REVERT: A   30 ARG cc_start: 0.1581 (OUTLIER) cc_final: 0.0954 (ppt90)
REVERT: A   66 PHE cc_start: 0.8081 (m-10) cc_final: 0.7795 (m-10)
REVERT: A  145 PHE cc_start: 0.7223 (m-80) cc_final: 0.6979 (m-80)
REVERT: A  196 MET cc_start: 0.8149 (mtp) cc_final: 0.7264 (mtm)
REVERT: A  222 ILE cc_start: 0.9068 (mt) cc_final: 0.8356 (mp)
REVERT: A  244 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6335 (mt)
REVERT: A  257 LYS cc_start: 0.9093 (mttp) cc_final: 0.8663 (mppt)
REVERT: A  305 ASP cc_start: 0.8554 (m-30) cc_final: 0.8092 (m-30)
REVERT: A  327 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7692 (mmm160)
REVERT: A  377 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7743 (mp0)
REVERT: A  387 MET cc_start: 0.7641 (mtm) cc_final: 0.6798 (mtm)
REVERT: A  411 MET cc_start: 0.8038 (mtp) cc_final: 0.7652 (mtp)
REVERT: A  454 ILE cc_start: 0.8599 (mt) cc_final: 0.8046 (mt)
REVERT: A  493 ILE cc_start: 0.8703 (mt) cc_final: 0.8487 (mp)
REVERT: A  617 VAL cc_start: 0.7798 (t) cc_final: 0.7527 (t)
REVERT: A  630 MET cc_start: 0.7885 (mtt) cc_final: 0.7202 (mmm)
REVERT: A  711 PHE cc_start: 0.7803 (t80) cc_final: 0.7587 (t80)
REVERT: A  731 MET cc_start: 0.9233 (tpt) cc_final: 0.9000 (mmm)
REVERT: A  763 MET cc_start: 0.8017 (tmm) cc_final: 0.7543 (tmm)
REVERT: A  765 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7631 (mt-10)
REVERT: Y   18 ILE cc_start: 0.8587 (mt) cc_final: 0.8379 (mt)
REVERT: Y  217 LEU cc_start: 0.9079 (mt) cc_final: 0.8582 (tp)
REVERT: Y  233 TYR cc_start: 0.8374 (t80) cc_final: 0.8019 (t80)
REVERT: Y  298 LEU cc_start: 0.8257 (mt) cc_final: 0.8016 (mm)
REVERT: Y  381 LEU cc_start: 0.8590 (tp) cc_final: 0.8218 (tt)
REVERT: E   24 LYS cc_start: 0.9297 (mmtt) cc_final: 0.9077 (ttpp)
  outliers start: 7
  outliers final: 1
  residues processed: 413
  average time/residue: 0.2617
  time to fit residues: 143.1972
Evaluate side-chains
  244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 241
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  364 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
A 238 ASN
A 291 ASN
A 297 HIS
A 347 ASN
A 383 ASN
A 513 HIS
A 529 GLN
A 536 GLN
A 613 GLN
A 736 GLN
A 739 HIS
Y  88 GLN
Y 101 GLN
Y 124 GLN
** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 134 ASN
Y 143 ASN
Y 177 ASN
Y 213 ASN
Y 267 ASN
Y 343 GLN
Y 387 ASN
Y 415 GLN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.142984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.112719 restraints weight = 24401.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.115508 restraints weight = 14778.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.116917 restraints weight = 8933.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  10065  Z= 0.205
  Angle     :  0.791  14.292  13594  Z= 0.419
  Chirality :  0.046   0.202   1555
  Planarity :  0.006   0.075   1740
  Dihedral  :  7.319 114.466   1372
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.64 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1235
  helix:  0.11 (0.18), residues: 798
  sheet: -0.93 (0.60), residues: 77
  loop : -1.92 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP Y 299 
 HIS   0.006   0.001   HIS A  93 
 PHE   0.041   0.002   PHE Y  67 
 TYR   0.017   0.002   TYR A 385 
 ARG   0.010   0.001   ARG A 750 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06453 (  630)
  hydrogen bonds       : angle       4.90511 ( 1860)
  covalent geometry    : bond        0.00445 (10064)
  covalent geometry    : angle       0.79117 (13594)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 252
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7785 (pt0) cc_final: 0.7507 (pt0)
REVERT: A   30 ARG cc_start: 0.1416 (OUTLIER) cc_final: 0.0639 (ppt170)
REVERT: A   79 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6625 (mmm)
REVERT: A   87 MET cc_start: 0.8485 (mmm) cc_final: 0.8259 (mmp)
REVERT: A  305 ASP cc_start: 0.8597 (m-30) cc_final: 0.8036 (m-30)
REVERT: A  365 GLU cc_start: 0.7864 (tt0) cc_final: 0.7592 (tm-30)
REVERT: A  367 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: A  380 GLU cc_start: 0.8511 (mp0) cc_final: 0.8078 (mp0)
REVERT: A  411 MET cc_start: 0.7975 (mtp) cc_final: 0.7657 (mtp)
REVERT: A  600 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7636 (t0)
REVERT: A  725 MET cc_start: 0.8599 (ptm) cc_final: 0.7956 (ptm)
REVERT: A  759 MET cc_start: 0.8540 (mmm) cc_final: 0.8217 (mmm)
REVERT: A  763 MET cc_start: 0.8463 (tmm) cc_final: 0.7931 (tmm)
REVERT: Y   24 MET cc_start: 0.8037 (mmp) cc_final: 0.7249 (mmp)
REVERT: Y  164 MET cc_start: 0.8699 (ptp) cc_final: 0.8441 (ptp)
REVERT: Y  217 LEU cc_start: 0.9094 (mt) cc_final: 0.8551 (tp)
REVERT: Y  233 TYR cc_start: 0.8420 (t80) cc_final: 0.8079 (t80)
REVERT: Y  298 LEU cc_start: 0.8306 (mt) cc_final: 0.8065 (tp)
REVERT: Y  343 GLN cc_start: 0.8006 (tp40) cc_final: 0.7730 (tp40)
REVERT: E   24 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8802 (ttpp)
  outliers start: 48
  outliers final: 20
  residues processed: 284
  average time/residue: 0.2112
  time to fit residues: 84.8393
Evaluate side-chains
  237 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 213
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   79 MET
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  647 GLU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain Y residue   42 ASP
Chi-restraints excluded: chain Y residue  156 LEU
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  370 VAL
Chi-restraints excluded: chain Y residue  383 VAL
Chi-restraints excluded: chain Y residue  420 LEU
Chi-restraints excluded: chain E residue   22 ASN
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 114 optimal weight:    0.3980
   chunk 56 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
A 202 HIS
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 464 HIS
A 753 GLN
** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.130505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101426 restraints weight = 24209.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.102941 restraints weight = 13238.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.104090 restraints weight = 9595.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  10065  Z= 0.184
  Angle     :  0.731   9.712  13594  Z= 0.382
  Chirality :  0.045   0.164   1555
  Planarity :  0.005   0.067   1740
  Dihedral  :  6.563 108.995   1368
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 20.45 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.23), residues: 1235
  helix:  0.83 (0.18), residues: 786
  sheet: -0.80 (0.57), residues: 79
  loop : -1.77 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 652 
 HIS   0.006   0.001   HIS A  93 
 PHE   0.027   0.002   PHE Y 184 
 TYR   0.023   0.002   TYR A 385 
 ARG   0.006   0.001   ARG Y  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06156 (  630)
  hydrogen bonds       : angle       4.61086 ( 1860)
  covalent geometry    : bond        0.00401 (10064)
  covalent geometry    : angle       0.73077 (13594)
  Misc. bond           : bond        0.00057 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 237
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7909 (pt0) cc_final: 0.7617 (pt0)
REVERT: A   70 ARG cc_start: 0.7434 (mmm160) cc_final: 0.7108 (ttt180)
REVERT: A  189 MET cc_start: 0.8302 (ttm) cc_final: 0.7952 (mtp)
REVERT: A  305 ASP cc_start: 0.8538 (m-30) cc_final: 0.7813 (m-30)
REVERT: A  327 ARG cc_start: 0.6177 (mmm160) cc_final: 0.5952 (mmm160)
REVERT: A  329 TYR cc_start: 0.8876 (m-10) cc_final: 0.8627 (m-10)
REVERT: A  363 MET cc_start: 0.8930 (ttm) cc_final: 0.8493 (ttm)
REVERT: A  365 GLU cc_start: 0.8171 (tt0) cc_final: 0.7846 (tm-30)
REVERT: A  384 ILE cc_start: 0.9258 (mp) cc_final: 0.9033 (mm)
REVERT: A  411 MET cc_start: 0.8136 (mtp) cc_final: 0.7880 (mtp)
REVERT: A  559 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6841 (m-30)
REVERT: A  586 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8197 (mm-30)
REVERT: A  666 LEU cc_start: 0.7832 (tp) cc_final: 0.7461 (tp)
REVERT: A  725 MET cc_start: 0.8511 (ptm) cc_final: 0.8165 (ptm)
REVERT: A  759 MET cc_start: 0.8720 (mmm) cc_final: 0.8424 (mmm)
REVERT: A  763 MET cc_start: 0.8718 (tmm) cc_final: 0.8351 (tmm)
REVERT: Y   24 MET cc_start: 0.8268 (mmp) cc_final: 0.7928 (mmm)
REVERT: Y  164 MET cc_start: 0.8717 (ptp) cc_final: 0.8253 (ptp)
REVERT: Y  184 PHE cc_start: 0.9442 (t80) cc_final: 0.9206 (t80)
REVERT: Y  217 LEU cc_start: 0.9120 (mt) cc_final: 0.8662 (tp)
REVERT: Y  218 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8360 (mm)
REVERT: Y  233 TYR cc_start: 0.8475 (t80) cc_final: 0.8045 (t80)
REVERT: E   24 LYS cc_start: 0.9345 (mmtt) cc_final: 0.9090 (ttpp)
  outliers start: 58
  outliers final: 31
  residues processed: 267
  average time/residue: 0.1985
  time to fit residues: 76.8911
Evaluate side-chains
  247 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 214
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain Y residue   74 VAL
Chi-restraints excluded: chain Y residue  126 LEU
Chi-restraints excluded: chain Y residue  156 LEU
Chi-restraints excluded: chain Y residue  166 LEU
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  218 LEU
Chi-restraints excluded: chain Y residue  278 VAL
Chi-restraints excluded: chain Y residue  378 ILE
Chi-restraints excluded: chain Y residue  383 VAL
Chi-restraints excluded: chain Y residue  420 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   27 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0870
   chunk 109 optimal weight:    0.0570
   chunk 117 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0270
   chunk 21 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
A  93 HIS
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
Y  66 ASN
Y 133 ASN
** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.133757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.104846 restraints weight = 24233.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.106147 restraints weight = 14075.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.107676 restraints weight = 10011.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.6153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  10065  Z= 0.149
  Angle     :  0.688   9.306  13594  Z= 0.355
  Chirality :  0.043   0.169   1555
  Planarity :  0.004   0.060   1740
  Dihedral  :  6.209 101.669   1368
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 22.24 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.24), residues: 1235
  helix:  1.15 (0.18), residues: 782
  sheet: -0.75 (0.56), residues: 85
  loop : -1.63 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 652 
 HIS   0.006   0.001   HIS A 283 
 PHE   0.023   0.001   PHE E   7 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 750 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05490 (  630)
  hydrogen bonds       : angle       4.37279 ( 1860)
  covalent geometry    : bond        0.00316 (10064)
  covalent geometry    : angle       0.68833 (13594)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 232
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7149 (ttt180)
REVERT: A  189 MET cc_start: 0.8115 (ttm) cc_final: 0.7893 (mtp)
REVERT: A  213 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8783 (tp)
REVERT: A  305 ASP cc_start: 0.8516 (m-30) cc_final: 0.7779 (m-30)
REVERT: A  327 ARG cc_start: 0.6100 (mmm160) cc_final: 0.5619 (mmp-170)
REVERT: A  380 GLU cc_start: 0.8809 (mp0) cc_final: 0.8544 (mp0)
REVERT: A  384 ILE cc_start: 0.9328 (mp) cc_final: 0.9074 (mm)
REVERT: A  409 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7220 (mtt-85)
REVERT: A  411 MET cc_start: 0.8106 (mtp) cc_final: 0.7866 (mtp)
REVERT: A  557 MET cc_start: 0.8144 (mpp) cc_final: 0.7847 (pmm)
REVERT: A  559 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7106 (m-30)
REVERT: A  586 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8174 (mm-30)
REVERT: A  600 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7522 (t0)
REVERT: A  630 MET cc_start: 0.7553 (mmt) cc_final: 0.7337 (mmt)
REVERT: A  636 GLU cc_start: 0.8604 (tp30) cc_final: 0.8387 (mt-10)
REVERT: A  684 MET cc_start: 0.8076 (mtt) cc_final: 0.7862 (mtt)
REVERT: A  725 MET cc_start: 0.8424 (ptm) cc_final: 0.8223 (ptm)
REVERT: A  759 MET cc_start: 0.8628 (mmm) cc_final: 0.8398 (mmm)
REVERT: A  763 MET cc_start: 0.8817 (tmm) cc_final: 0.7951 (tmm)
REVERT: Y   30 ILE cc_start: 0.8906 (tp) cc_final: 0.8653 (pt)
REVERT: Y   46 LEU cc_start: 0.7667 (mt) cc_final: 0.7419 (pp)
REVERT: Y   88 GLN cc_start: 0.8543 (pp30) cc_final: 0.8317 (tm-30)
REVERT: Y  164 MET cc_start: 0.8780 (ptp) cc_final: 0.8241 (ptp)
REVERT: Y  217 LEU cc_start: 0.9020 (mt) cc_final: 0.8590 (tt)
REVERT: Y  233 TYR cc_start: 0.8398 (t80) cc_final: 0.7976 (t80)
REVERT: E   14 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8618 (mm-30)
REVERT: E   17 LYS cc_start: 0.9254 (mtmm) cc_final: 0.8845 (mppt)
REVERT: E   23 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7916 (mpt180)
REVERT: E   24 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9002 (ttpp)
  outliers start: 52
  outliers final: 23
  residues processed: 262
  average time/residue: 0.1989
  time to fit residues: 75.5372
Evaluate side-chains
  244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 216
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain Y residue  126 LEU
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  156 LEU
Chi-restraints excluded: chain Y residue  166 LEU
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  287 ILE
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 142 GLN
** Y 261 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 = 0.3902 r_free = 0.3902 target = 0.128387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.099166 restraints weight = 24185.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.099756 restraints weight = 14218.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.100847 restraints weight = 10706.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.6827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10065  Z= 0.172
  Angle     :  0.689   7.822  13594  Z= 0.359
  Chirality :  0.043   0.181   1555
  Planarity :  0.005   0.059   1740
  Dihedral  :  6.082 100.546   1368
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 24.41 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1235
  helix:  1.38 (0.18), residues: 784
  sheet: -0.65 (0.54), residues: 96
  loop : -1.57 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP Y 299 
 HIS   0.004   0.001   HIS A  43 
 PHE   0.029   0.001   PHE Y 184 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.012   0.001   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05739 (  630)
  hydrogen bonds       : angle       4.34486 ( 1860)
  covalent geometry    : bond        0.00377 (10064)
  covalent geometry    : angle       0.68947 (13594)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 221
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ASP cc_start: 0.7522 (p0) cc_final: 0.7206 (t0)
REVERT: A   70 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7475 (ttt180)
REVERT: A  127 VAL cc_start: 0.9488 (t) cc_final: 0.9153 (m)
REVERT: A  146 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7797 (tm-30)
REVERT: A  173 THR cc_start: 0.9248 (m) cc_final: 0.8855 (p)
REVERT: A  305 ASP cc_start: 0.8362 (m-30) cc_final: 0.7746 (m-30)
REVERT: A  324 MET cc_start: 0.7788 (mtp) cc_final: 0.7324 (ttp)
REVERT: A  380 GLU cc_start: 0.8915 (mp0) cc_final: 0.8577 (mp0)
REVERT: A  409 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6552 (mtt-85)
REVERT: A  411 MET cc_start: 0.8321 (mtp) cc_final: 0.7998 (mtp)
REVERT: A  443 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: A  546 MET cc_start: 0.8280 (ttm) cc_final: 0.7610 (ttm)
REVERT: A  555 MET cc_start: 0.8531 (mmt) cc_final: 0.8271 (mpp)
REVERT: A  586 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8303 (mm-30)
REVERT: A  600 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7622 (t0)
REVERT: A  630 MET cc_start: 0.7838 (mmt) cc_final: 0.7591 (mmt)
REVERT: A  759 MET cc_start: 0.8727 (mmm) cc_final: 0.8508 (mmm)
REVERT: A  763 MET cc_start: 0.8883 (tmm) cc_final: 0.8363 (tmm)
REVERT: Y   24 MET cc_start: 0.8654 (mmm) cc_final: 0.7965 (mmm)
REVERT: Y   30 ILE cc_start: 0.8869 (tp) cc_final: 0.8664 (pt)
REVERT: Y  164 MET cc_start: 0.8752 (ptp) cc_final: 0.8267 (ptp)
REVERT: Y  217 LEU cc_start: 0.9021 (mt) cc_final: 0.8613 (tt)
REVERT: Y  218 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8412 (mm)
REVERT: Y  233 TYR cc_start: 0.8441 (t80) cc_final: 0.8026 (t80)
REVERT: Y  391 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8231 (tt)
REVERT: E    9 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8485 (mttt)
REVERT: E   23 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7963 (mpt180)
REVERT: E   24 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9015 (ttpp)
  outliers start: 46
  outliers final: 28
  residues processed: 247
  average time/residue: 0.2067
  time to fit residues: 73.6810
Evaluate side-chains
  237 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain Y residue  126 LEU
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  156 LEU
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  218 LEU
Chi-restraints excluded: chain Y residue  261 HIS
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  391 LEU
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 GLN
** Y 261 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 = 0.3885 r_free = 0.3885 target = 0.126840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.097589 restraints weight = 24223.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.098621 restraints weight = 13794.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.099658 restraints weight = 10147.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.7296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10065  Z= 0.157
  Angle     :  0.674   9.057  13594  Z= 0.348
  Chirality :  0.043   0.227   1555
  Planarity :  0.004   0.060   1740
  Dihedral  :  5.956  95.942   1368
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.30 %
    Favored  : 69.56 %
  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:  0.78 (0.24), residues: 1235
  helix:  1.53 (0.18), residues: 784
  sheet: -0.45 (0.56), residues: 94
  loop : -1.49 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  20 
 HIS   0.003   0.001   HIS A 297 
 PHE   0.021   0.001   PHE Y 184 
 TYR   0.012   0.001   TYR A 250 
 ARG   0.007   0.000   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05497 (  630)
  hydrogen bonds       : angle       4.24366 ( 1860)
  covalent geometry    : bond        0.00340 (10064)
  covalent geometry    : angle       0.67356 (13594)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 226
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7535 (ttt180)
REVERT: A  127 VAL cc_start: 0.9474 (t) cc_final: 0.9129 (m)
REVERT: A  146 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: A  173 THR cc_start: 0.9271 (m) cc_final: 0.8881 (p)
REVERT: A  305 ASP cc_start: 0.8331 (m-30) cc_final: 0.7682 (m-30)
REVERT: A  324 MET cc_start: 0.7784 (mtp) cc_final: 0.7308 (ttp)
REVERT: A  380 GLU cc_start: 0.8847 (mp0) cc_final: 0.8580 (mp0)
REVERT: A  409 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7472 (mtt-85)
REVERT: A  443 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: A  555 MET cc_start: 0.8695 (mmt) cc_final: 0.8440 (mpp)
REVERT: A  561 PHE cc_start: 0.7897 (m-80) cc_final: 0.7573 (m-80)
REVERT: A  586 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8342 (mm-30)
REVERT: A  600 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7587 (t0)
REVERT: A  630 MET cc_start: 0.8475 (mmt) cc_final: 0.8146 (mmt)
REVERT: A  632 LYS cc_start: 0.8829 (mttp) cc_final: 0.8325 (mtmm)
REVERT: A  689 MET cc_start: 0.8256 (tpp) cc_final: 0.7770 (mmt)
REVERT: A  763 MET cc_start: 0.8870 (tmm) cc_final: 0.8392 (tmm)
REVERT: Y    8 PHE cc_start: 0.8389 (m-10) cc_final: 0.7855 (m-10)
REVERT: Y   24 MET cc_start: 0.8683 (mmm) cc_final: 0.8100 (mmm)
REVERT: Y   30 ILE cc_start: 0.8840 (tp) cc_final: 0.8619 (pt)
REVERT: Y  164 MET cc_start: 0.8760 (ptp) cc_final: 0.8273 (ptp)
REVERT: Y  217 LEU cc_start: 0.9016 (mt) cc_final: 0.8651 (tt)
REVERT: Y  233 TYR cc_start: 0.8439 (t80) cc_final: 0.8017 (t80)
REVERT: Y  417 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7864 (mt-10)
REVERT: E    9 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8439 (mttt)
REVERT: E   23 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8006 (mpt180)
REVERT: E   24 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8902 (ttpp)
  outliers start: 44
  outliers final: 30
  residues processed: 248
  average time/residue: 0.2075
  time to fit residues: 74.1680
Evaluate side-chains
  239 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 206
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain Y residue   36 VAL
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  156 LEU
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  238 PHE
Chi-restraints excluded: chain Y residue  370 VAL
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 117 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 124 GLN
** Y 261 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 = 0.3821 r_free = 0.3821 target = 0.122284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.094939 restraints weight = 23692.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.095390 restraints weight = 13994.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.096678 restraints weight = 10017.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.7767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10065  Z= 0.163
  Angle     :  0.706  14.830  13594  Z= 0.356
  Chirality :  0.044   0.247   1555
  Planarity :  0.005   0.057   1740
  Dihedral  :  5.883  94.318   1368
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 27.90 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1235
  helix:  1.59 (0.18), residues: 778
  sheet: -0.50 (0.59), residues: 83
  loop : -1.32 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP Y 299 
 HIS   0.003   0.001   HIS A 739 
 PHE   0.038   0.001   PHE Y 184 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.008   0.001   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05640 (  630)
  hydrogen bonds       : angle       4.26107 ( 1860)
  covalent geometry    : bond        0.00355 (10064)
  covalent geometry    : angle       0.70620 (13594)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 224
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 VAL cc_start: 0.9477 (t) cc_final: 0.9111 (m)
REVERT: A  146 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7493 (tm-30)
REVERT: A  173 THR cc_start: 0.9291 (m) cc_final: 0.8888 (p)
REVERT: A  305 ASP cc_start: 0.8313 (m-30) cc_final: 0.7630 (m-30)
REVERT: A  324 MET cc_start: 0.7788 (mtp) cc_final: 0.7450 (ttt)
REVERT: A  367 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8755 (pp)
REVERT: A  380 GLU cc_start: 0.8755 (mp0) cc_final: 0.8389 (mp0)
REVERT: A  409 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7636 (mtt-85)
REVERT: A  443 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: A  541 MET cc_start: 0.8753 (tpp) cc_final: 0.8357 (tpp)
REVERT: A  555 MET cc_start: 0.8742 (mmt) cc_final: 0.8505 (mpp)
REVERT: A  586 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8239 (mm-30)
REVERT: A  600 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7589 (t0)
REVERT: A  630 MET cc_start: 0.8550 (mmt) cc_final: 0.8170 (mmt)
REVERT: A  666 LEU cc_start: 0.7681 (tp) cc_final: 0.7275 (tt)
REVERT: A  689 MET cc_start: 0.8370 (tpp) cc_final: 0.7734 (mmt)
REVERT: A  763 MET cc_start: 0.8880 (tmm) cc_final: 0.8366 (tmm)
REVERT: A  774 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6313 (t80)
REVERT: Y   24 MET cc_start: 0.8698 (mmm) cc_final: 0.8292 (mmm)
REVERT: Y  164 MET cc_start: 0.8765 (ptp) cc_final: 0.8271 (ptp)
REVERT: Y  217 LEU cc_start: 0.9053 (mt) cc_final: 0.8647 (tt)
REVERT: Y  218 LEU cc_start: 0.9177 (pp) cc_final: 0.8764 (mm)
REVERT: Y  233 TYR cc_start: 0.8446 (t80) cc_final: 0.7997 (t80)
REVERT: Y  417 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7856 (mt-10)
REVERT: E    9 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8339 (mtmm)
REVERT: E   23 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7977 (mpt180)
REVERT: E   24 LYS cc_start: 0.9211 (mmtt) cc_final: 0.8908 (ttpp)
  outliers start: 45
  outliers final: 29
  residues processed: 249
  average time/residue: 0.2070
  time to fit residues: 74.0264
Evaluate side-chains
  243 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  774 PHE
Chi-restraints excluded: chain Y residue   36 VAL
Chi-restraints excluded: chain Y residue   55 VAL
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  220 VAL
Chi-restraints excluded: chain Y residue  370 VAL
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0060
   chunk 5 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
A 739 HIS
Y 101 GLN
** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093675 restraints weight = 24606.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.094425 restraints weight = 14775.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.095609 restraints weight = 10524.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.8144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10065  Z= 0.159
  Angle     :  0.736  12.537  13594  Z= 0.367
  Chirality :  0.045   0.283   1555
  Planarity :  0.004   0.056   1740
  Dihedral  :  5.846  92.121   1368
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 29.88 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1235
  helix:  1.61 (0.18), residues: 775
  sheet: -0.55 (0.55), residues: 93
  loop : -1.34 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP Y  98 
 HIS   0.003   0.001   HIS A 739 
 PHE   0.022   0.001   PHE Y 184 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.007   0.000   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05578 (  630)
  hydrogen bonds       : angle       4.24275 ( 1860)
  covalent geometry    : bond        0.00352 (10064)
  covalent geometry    : angle       0.73559 (13594)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 218
  time to evaluate  : 1.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7456 (mt0)
REVERT: A  127 VAL cc_start: 0.9431 (t) cc_final: 0.9067 (m)
REVERT: A  173 THR cc_start: 0.9307 (m) cc_final: 0.8922 (p)
REVERT: A  305 ASP cc_start: 0.8327 (m-30) cc_final: 0.7639 (m-30)
REVERT: A  324 MET cc_start: 0.7722 (mtp) cc_final: 0.7371 (ttt)
REVERT: A  327 ARG cc_start: 0.6351 (mmm160) cc_final: 0.3847 (tpt170)
REVERT: A  380 GLU cc_start: 0.8791 (mp0) cc_final: 0.8448 (mp0)
REVERT: A  409 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7731 (mtt-85)
REVERT: A  443 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7596 (tm-30)
REVERT: A  555 MET cc_start: 0.8616 (mmt) cc_final: 0.8307 (mpp)
REVERT: A  586 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8424 (mm-30)
REVERT: A  600 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7546 (t0)
REVERT: A  630 MET cc_start: 0.8606 (mmt) cc_final: 0.8271 (mmt)
REVERT: A  632 LYS cc_start: 0.8857 (pttm) cc_final: 0.8642 (mtmm)
REVERT: A  666 LEU cc_start: 0.7819 (tp) cc_final: 0.7444 (tp)
REVERT: A  689 MET cc_start: 0.8415 (tpp) cc_final: 0.7848 (mmt)
REVERT: A  763 MET cc_start: 0.8923 (tmm) cc_final: 0.8384 (tmm)
REVERT: Y   24 MET cc_start: 0.8729 (mmm) cc_final: 0.8278 (mmm)
REVERT: Y   98 TRP cc_start: 0.8209 (m-10) cc_final: 0.7672 (m-10)
REVERT: Y  164 MET cc_start: 0.8642 (ptp) cc_final: 0.8185 (ptp)
REVERT: Y  217 LEU cc_start: 0.9023 (mt) cc_final: 0.8665 (tt)
REVERT: Y  218 LEU cc_start: 0.9136 (pp) cc_final: 0.8804 (mm)
REVERT: Y  233 TYR cc_start: 0.8427 (t80) cc_final: 0.7952 (t80)
REVERT: Y  417 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7880 (mt-10)
REVERT: E    9 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8347 (mtmm)
REVERT: E   24 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8971 (ttpp)
REVERT: E   25 GLU cc_start: 0.8962 (pm20) cc_final: 0.8688 (pm20)
  outliers start: 35
  outliers final: 29
  residues processed: 235
  average time/residue: 0.2044
  time to fit residues: 69.3476
Evaluate side-chains
  235 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 203
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Y residue   36 VAL
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  238 PHE
Chi-restraints excluded: chain Y residue  370 VAL
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  421 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 95 optimal weight:    0.2980
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 HIS
** Y 261 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 = 0.3814 r_free = 0.3814 target = 0.121483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.093512 restraints weight = 24464.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.094250 restraints weight = 14458.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.095427 restraints weight = 10430.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.8435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10065  Z= 0.153
  Angle     :  0.744  12.492  13594  Z= 0.364
  Chirality :  0.045   0.392   1555
  Planarity :  0.004   0.057   1740
  Dihedral  :  5.756  90.420   1368
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 30.25 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.02 (0.24), residues: 1235
  helix:  1.75 (0.18), residues: 772
  sheet: -0.53 (0.55), residues: 93
  loop : -1.31 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP Y  98 
 HIS   0.003   0.001   HIS A 739 
 PHE   0.032   0.001   PHE Y 184 
 TYR   0.023   0.001   TYR A 665 
 ARG   0.009   0.000   ARG A 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05445 (  630)
  hydrogen bonds       : angle       4.19204 ( 1860)
  covalent geometry    : bond        0.00339 (10064)
  covalent geometry    : angle       0.74355 (13594)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 216
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 VAL cc_start: 0.9414 (t) cc_final: 0.9057 (m)
REVERT: A  173 THR cc_start: 0.9313 (m) cc_final: 0.8927 (p)
REVERT: A  305 ASP cc_start: 0.8293 (m-30) cc_final: 0.7589 (m-30)
REVERT: A  324 MET cc_start: 0.7667 (mtp) cc_final: 0.7324 (ttt)
REVERT: A  327 ARG cc_start: 0.5985 (mmm160) cc_final: 0.3990 (tpt170)
REVERT: A  380 GLU cc_start: 0.8762 (mp0) cc_final: 0.8363 (mp0)
REVERT: A  409 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7685 (mtt-85)
REVERT: A  443 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: A  555 MET cc_start: 0.8593 (mmt) cc_final: 0.8253 (mpp)
REVERT: A  586 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8439 (mm-30)
REVERT: A  600 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (t0)
REVERT: A  630 MET cc_start: 0.8598 (mmt) cc_final: 0.8236 (mmt)
REVERT: A  666 LEU cc_start: 0.7819 (tp) cc_final: 0.7444 (tp)
REVERT: A  685 LEU cc_start: 0.8544 (mm) cc_final: 0.8239 (pp)
REVERT: A  689 MET cc_start: 0.8455 (tpp) cc_final: 0.7950 (mmt)
REVERT: A  725 MET cc_start: 0.8290 (ptm) cc_final: 0.7908 (tmm)
REVERT: A  738 ILE cc_start: 0.8908 (tp) cc_final: 0.8612 (tp)
REVERT: A  759 MET cc_start: 0.8801 (mtt) cc_final: 0.8580 (mmm)
REVERT: A  763 MET cc_start: 0.8853 (tmm) cc_final: 0.8281 (tmm)
REVERT: Y   24 MET cc_start: 0.8805 (mmm) cc_final: 0.8355 (mmm)
REVERT: Y   98 TRP cc_start: 0.8277 (m-10) cc_final: 0.7868 (m-90)
REVERT: Y  164 MET cc_start: 0.8601 (ptp) cc_final: 0.8186 (ptp)
REVERT: Y  217 LEU cc_start: 0.9014 (mt) cc_final: 0.8660 (tt)
REVERT: Y  218 LEU cc_start: 0.9140 (pp) cc_final: 0.8806 (mm)
REVERT: Y  233 TYR cc_start: 0.8396 (t80) cc_final: 0.7912 (t80)
REVERT: Y  417 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7891 (mt-10)
REVERT: E    9 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8349 (mtmm)
REVERT: E   24 LYS cc_start: 0.9221 (mmtt) cc_final: 0.8925 (ttpp)
  outliers start: 37
  outliers final: 30
  residues processed: 234
  average time/residue: 0.2589
  time to fit residues: 88.9105
Evaluate side-chains
  228 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  595 GLN
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain Y residue   36 VAL
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  400 THR
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 19 optimal weight:    0.0270
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 103 optimal weight:    0.0040
   chunk 97 optimal weight:    0.9990
   chunk 105 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.3452

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 HIS
** Y 261 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 = 0.3815 r_free = 0.3815 target = 0.121794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.094186 restraints weight = 24267.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.094875 restraints weight = 13854.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.096038 restraints weight = 10240.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.8576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10065  Z= 0.148
  Angle     :  0.774  14.217  13594  Z= 0.375
  Chirality :  0.045   0.419   1555
  Planarity :  0.004   0.055   1740
  Dihedral  :  5.703  88.689   1368
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 30.25 %
    Favored  : 66.45 %
  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:  1.03 (0.24), residues: 1235
  helix:  1.73 (0.18), residues: 775
  sheet: -0.43 (0.55), residues: 93
  loop : -1.28 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP Y  98 
 HIS   0.008   0.001   HIS A 739 
 PHE   0.035   0.001   PHE Y 184 
 TYR   0.024   0.001   TYR A 665 
 ARG   0.007   0.000   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05290 (  630)
  hydrogen bonds       : angle       4.14778 ( 1860)
  covalent geometry    : bond        0.00324 (10064)
  covalent geometry    : angle       0.77379 (13594)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 209
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 VAL cc_start: 0.9463 (t) cc_final: 0.9098 (m)
REVERT: A  173 THR cc_start: 0.9310 (m) cc_final: 0.8933 (p)
REVERT: A  305 ASP cc_start: 0.8267 (m-30) cc_final: 0.7581 (m-30)
REVERT: A  380 GLU cc_start: 0.8805 (mp0) cc_final: 0.8404 (mp0)
REVERT: A  409 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7675 (mtt-85)
REVERT: A  443 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7504 (tm-30)
REVERT: A  555 MET cc_start: 0.8454 (mmt) cc_final: 0.8052 (mpp)
REVERT: A  563 MET cc_start: 0.6715 (ptm) cc_final: 0.6460 (ptm)
REVERT: A  586 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8423 (mm-30)
REVERT: A  600 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7448 (t0)
REVERT: A  630 MET cc_start: 0.8568 (mmt) cc_final: 0.8237 (mmt)
REVERT: A  632 LYS cc_start: 0.8916 (pttm) cc_final: 0.8506 (mtmm)
REVERT: A  666 LEU cc_start: 0.7711 (tp) cc_final: 0.7319 (tp)
REVERT: A  685 LEU cc_start: 0.8606 (mm) cc_final: 0.8221 (pp)
REVERT: A  689 MET cc_start: 0.8500 (tpp) cc_final: 0.8069 (mmt)
REVERT: A  738 ILE cc_start: 0.8940 (tp) cc_final: 0.8709 (tp)
REVERT: A  763 MET cc_start: 0.8851 (tmm) cc_final: 0.8293 (tmm)
REVERT: A  774 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.6191 (t80)
REVERT: A  776 MET cc_start: 0.8107 (tpp) cc_final: 0.7792 (tpp)
REVERT: Y   24 MET cc_start: 0.8859 (mmm) cc_final: 0.8428 (mmm)
REVERT: Y   98 TRP cc_start: 0.8226 (m-10) cc_final: 0.7881 (m-90)
REVERT: Y  164 MET cc_start: 0.8561 (ptp) cc_final: 0.8156 (ptp)
REVERT: Y  217 LEU cc_start: 0.9016 (mt) cc_final: 0.8685 (tt)
REVERT: Y  218 LEU cc_start: 0.9139 (pp) cc_final: 0.8798 (mm)
REVERT: Y  233 TYR cc_start: 0.8379 (t80) cc_final: 0.7894 (t80)
REVERT: Y  299 TRP cc_start: 0.8465 (t-100) cc_final: 0.8209 (t60)
REVERT: Y  417 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7911 (mt-10)
REVERT: E    9 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8349 (mtmm)
REVERT: E   23 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8012 (mpt180)
REVERT: E   24 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8892 (ttpp)
  outliers start: 35
  outliers final: 25
  residues processed: 227
  average time/residue: 0.3230
  time to fit residues: 106.7824
Evaluate side-chains
  231 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 2.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  746 THR
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  764 ILE
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  774 PHE
Chi-restraints excluded: chain Y residue  128 MET
Chi-restraints excluded: chain Y residue  171 THR
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  370 VAL
Chi-restraints excluded: chain Y residue  385 PHE
Chi-restraints excluded: chain Y residue  400 THR
Chi-restraints excluded: chain Y residue  421 VAL
Chi-restraints excluded: chain E residue   23 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 103 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 HIS
** Y 261 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 = 0.3795 r_free = 0.3795 target = 0.120419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.093025 restraints weight = 24500.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.093842 restraints weight = 14135.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095044 restraints weight = 10147.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.8888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10065  Z= 0.156
  Angle     :  0.780  13.933  13594  Z= 0.380
  Chirality :  0.045   0.417   1555
  Planarity :  0.005   0.056   1740
  Dihedral  :  5.697  89.151   1368
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 31.20 %
    Favored  : 65.88 %
  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:  1.07 (0.25), residues: 1235
  helix:  1.74 (0.19), residues: 778
  sheet: -0.06 (0.57), residues: 86
  loop : -1.35 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP Y  98 
 HIS   0.003   0.001   HIS A 739 
 PHE   0.030   0.001   PHE E  43 
 TYR   0.024   0.001   TYR A 665 
 ARG   0.008   0.000   ARG E  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05417 (  630)
  hydrogen bonds       : angle       4.21465 ( 1860)
  covalent geometry    : bond        0.00346 (10064)
  covalent geometry    : angle       0.78012 (13594)
  Misc. bond           : bond        0.00001 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3679.16 seconds
wall clock time: 66 minutes 48.99 seconds (4008.99 seconds total)