Starting phenix.real_space_refine
on Fri Feb 14 22:34:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q49_13799/02_2025/7q49_13799_trim.cif"
  }
  resolution = 3.72
  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=   0.003 sd=   0.059
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      19      5.16       5
     C    3398      2.51       5
     N     873      2.21       5
     O    1045      1.98       5
     H    4788      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10124
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 9804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 9804
          Classifications: {'peptide': 616}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 577}
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 32
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.09, per 1000 atoms: 0.50
  Number of scatterers: 10124
  At special positions: 0
  Unit cell: (77.38, 89.04, 93.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      19     16.00
     O    1045      8.00
     N     873      7.00
     C    3398      6.00
     H    4788      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 330 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 528 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   5 "
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1302 " - " ASN A  82 "
      " NAG A1303 " - " ASN A 416 "
      " NAG B   1 " - " ASN A  25 "
      " NAG C   1 " - " ASN A 289 "
      " NAG D   1 " - " ASN A   9 "
      " NAG E   1 " - " ASN A 117 "
      " NAG F   1 " - " ASN A  45 "
      " NAG G   1 " - " ASN A 480 "
  Time building additional restraints: 3.16
  Conformation dependent library (CDL) restraints added in 710.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1301 "
        pdb="ZN    ZN A1301 " - pdb=" NE2 HIS A 365 "
        pdb="ZN    ZN A1301 " - pdb=" NE2 HIS A 361 "


  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      70.3% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 45
      removed outlier: 3.804A  pdb=" N   GLN A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 77
      removed outlier: 3.758A  pdb=" N   GLU A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 85 through 97
    Processing helix  chain 'A' and resid 98 through 103
      removed outlier: 3.583A  pdb=" N   ALA A 101 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 125
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 152 through 190
      Proline residue:  A 170  - end of helix
      Proline residue:  A 173  - end of helix
      removed outlier: 3.644A  pdb=" N   GLU A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 188 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 201
      removed outlier: 3.803A  pdb=" N   TRP A 201 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 238
      Proline residue:  A 220  - end of helix
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 261 through 263
      No H-bonds generated for 'chain 'A' and resid 261 through 263'
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 279 through 286
      removed outlier: 3.578A  pdb=" N   GLN A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.620A  pdb=" N   ARG A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
      removed outlier: 3.966A  pdb=" N   TRP A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 373
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 386 through 401
      removed outlier: 3.590A  pdb=" N   GLY A 392 " --> pdb=" O   HIS A 388 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 417 through 433
    Processing helix  chain 'A' and resid 434 through 452
      removed outlier: 4.473A  pdb=" N   PHE A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 472
      removed outlier: 3.557A  pdb=" N   TRP A 463 " --> pdb=" O   TYR A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.682A  pdb=" N   PHE A 502 " --> pdb=" O   TYR A 498 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 509 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
    Processing helix  chain 'A' and resid 533 through 547
      removed outlier: 3.526A  pdb=" N   LYS A 539 " --> pdb=" O   LYS A 535 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 567 through 574
    Processing helix  chain 'A' and resid 574 through 589
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127
    Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249
      removed outlier: 6.065A  pdb=" N   ILE A 248 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 336

    294 hydrogen bonds defined for protein.
    843 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: 3.66

  Time building geometry restraints manager: 3.69 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 4787
        1.04 -     1.24: 587
        1.24 -     1.44: 1914
        1.44 -     1.63: 2960
        1.63 -     1.83: 31
  Bond restraints: 10279
  Sorted by residual:
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.358  0.048 2.00e-02 2.50e+03 5.71e+00
  bond pdb=" C5  BMA F   3 "
       pdb=" O5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.463 -0.046 2.00e-02 2.50e+03 5.28e+00
  bond pdb=" C1  MAN B   4 "
       pdb=" C2  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.568 -0.042 2.00e-02 2.50e+03 4.44e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" C2  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.532  1.491  0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.366  0.040 2.00e-02 2.50e+03 3.95e+00
  ... (remaining 10274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17208
        1.59 -     3.17: 956
        3.17 -     4.76: 158
        4.76 -     6.35: 29
        6.35 -     7.93: 9
  Bond angle restraints: 18360
  Sorted by residual:
  angle pdb=" C   LYS A 341 "
        pdb=" N   ASP A 342 "
        pdb=" CA  ASP A 342 "
      ideal   model   delta    sigma   weight residual
     121.62  115.31    6.31 1.83e+00 2.99e-01 1.19e+01
  angle pdb=" N   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" C   LYS A 321 "
      ideal   model   delta    sigma   weight residual
     109.81  102.50    7.31 2.21e+00 2.05e-01 1.09e+01
  angle pdb=" CA  TYR A 338 "
        pdb=" CB  TYR A 338 "
        pdb=" CG  TYR A 338 "
      ideal   model   delta    sigma   weight residual
     113.90  108.25    5.65 1.80e+00 3.09e-01 9.85e+00
  angle pdb=" N   THR A 349 "
        pdb=" CA  THR A 349 "
        pdb=" C   THR A 349 "
      ideal   model   delta    sigma   weight residual
     110.23  114.52   -4.29 1.45e+00 4.76e-01 8.77e+00
  angle pdb=" N   PHE A  83 "
        pdb=" CA  PHE A  83 "
        pdb=" CB  PHE A  83 "
      ideal   model   delta    sigma   weight residual
     109.48  113.98   -4.50 1.55e+00 4.16e-01 8.42e+00
  ... (remaining 18355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.35: 4789
       21.35 -    42.69: 288
       42.69 -    64.04: 98
       64.04 -    85.39: 49
       85.39 -   106.73: 29
  Dihedral angle restraints: 5253
    sinusoidal: 2996
      harmonic: 2257
  Sorted by residual:
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.02  106.73     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C3  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -57.53  105.15     1      3.00e+01 1.11e-03 1.35e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -175.74  104.45     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 5250 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 682
       0.066 -    0.132: 146
       0.132 -    0.198: 14
       0.198 -    0.264: 5
       0.264 -    0.330: 7
  Chirality restraints: 854
  Sorted by residual:
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.60    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.59    0.32 2.00e-01 2.50e+01 2.51e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.58    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 851 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 508 "   -0.046 2.00e-02 2.50e+03   5.32e-02 4.25e+01
        pdb=" CD  GLN A 508 "    0.050 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 508 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 508 "    0.077 2.00e-02 2.50e+03
        pdb="HE21 GLN A 508 "    0.003 2.00e-02 2.50e+03
        pdb="HE22 GLN A 508 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 479 "   -0.130 9.50e-02 1.11e+02   5.15e-02 1.91e+01
        pdb=" NE  ARG A 479 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 479 "   -0.039 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 479 "   -0.039 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 479 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG A 479 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 479 "    0.045 2.00e-02 2.50e+03
        pdb="HH21 ARG A 479 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 479 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 371 "    0.028 2.00e-02 2.50e+03   3.34e-02 1.67e+01
        pdb=" CD  GLN A 371 "   -0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 371 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 371 "   -0.051 2.00e-02 2.50e+03
        pdb="HE21 GLN A 371 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A 371 "    0.050 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 309
        2.14 -     2.76: 18476
        2.76 -     3.37: 28899
        3.37 -     3.99: 35865
        3.99 -     4.60: 56711
  Nonbonded interactions: 140260
  Sorted by model distance:
  nonbonded pdb=" HG1 THR A 454 "
            pdb=" OD2 ASP A 462 "
     model   vdw
     1.526 2.450
  nonbonded pdb=" HG1 THR A 468 "
            pdb=" O   ILE A 473 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HH  TYR A 521 "
            pdb=" O   PRO A 524 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" O   TRP A  40 "
            pdb=" HG1 THR A  44 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD2 ASP A 443 "
            pdb=" H   ILE A 499 "
     model   vdw
     1.594 2.450
  ... (remaining 140255 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:             0.190
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     29.230
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
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      :  0.008   0.048   5491  Z= 0.547
  Angle     :  1.081   7.934   7484  Z= 0.569
  Chirality :  0.061   0.330    854
  Planarity :  0.009   0.105    935
  Dihedral  : 19.174 106.734   2370
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.70 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.50 (0.30), residues: 614
  helix: -0.60 (0.22), residues: 367
  sheet: -0.97 (1.76), residues: 10
  loop : -1.48 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.006   TRP A 257 
 HIS   0.010   0.003   HIS A 331 
 PHE   0.028   0.004   PHE A 509 
 TYR   0.032   0.005   TYR A 338 
 ARG   0.031   0.005   ARG A 479 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.793 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLU cc_start: 0.8231 (pt0) cc_final: 0.8019 (tt0)
REVERT: A   52 ARG cc_start: 0.8909 (tpt170) cc_final: 0.8677 (ttp-110)
REVERT: A   64 PHE cc_start: 0.7995 (t80) cc_final: 0.7661 (t80)
REVERT: A  132 LYS cc_start: 0.8260 (tttt) cc_final: 0.7988 (mmmt)
REVERT: A  155 MET cc_start: 0.8060 (tpt) cc_final: 0.7768 (tpt)
REVERT: A  156 LEU cc_start: 0.9086 (tp) cc_final: 0.8769 (tp)
REVERT: A  182 SER cc_start: 0.9198 (t) cc_final: 0.8765 (m)
REVERT: A  183 ASN cc_start: 0.8341 (m-40) cc_final: 0.8080 (t0)
REVERT: A  298 GLU cc_start: 0.8454 (tt0) cc_final: 0.7972 (tm-30)
REVERT: A  302 THR cc_start: 0.9124 (p) cc_final: 0.8425 (p)
REVERT: A  341 LYS cc_start: 0.7998 (mttt) cc_final: 0.7673 (mmpt)
REVERT: A  350 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7386 (ttm170)
REVERT: A  453 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6909 (tmm160)
REVERT: A  579 GLN cc_start: 0.7818 (tt0) cc_final: 0.7450 (tm-30)
REVERT: A  592 LEU cc_start: 0.8423 (mt) cc_final: 0.8166 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.4687
  time to fit residues: 71.8981
Evaluate side-chains
  81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
A 292 HIS
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 GLN
A 575 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.114830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095615 restraints weight = 27056.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.100548 restraints weight = 10410.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.103625 restraints weight = 5332.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5491  Z= 0.244
  Angle     :  0.792   9.870   7484  Z= 0.414
  Chirality :  0.044   0.233    854
  Planarity :  0.006   0.046    935
  Dihedral  : 14.480  72.617   1180
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.87 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.05 (0.32), residues: 614
  helix:  0.57 (0.25), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.73 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 552 
 HIS   0.011   0.002   HIS A 360 
 PHE   0.030   0.002   PHE A 294 
 TYR   0.017   0.002   TYR A 215 
 ARG   0.003   0.001   ARG A 151 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.732 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8651 (ttp-110)
REVERT: A  132 LYS cc_start: 0.8184 (tttt) cc_final: 0.7915 (mmmt)
REVERT: A  161 GLU cc_start: 0.8321 (tt0) cc_final: 0.7971 (tt0)
REVERT: A  182 SER cc_start: 0.9104 (t) cc_final: 0.8694 (m)
REVERT: A  183 ASN cc_start: 0.8298 (m-40) cc_final: 0.7952 (t0)
REVERT: A  350 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7249 (ttm170)
REVERT: A  379 LEU cc_start: 0.8087 (mt) cc_final: 0.7749 (mt)
REVERT: A  453 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6870 (tmm160)
REVERT: A  462 ASP cc_start: 0.8050 (m-30) cc_final: 0.7191 (t0)
REVERT: A  582 GLN cc_start: 0.7865 (mt0) cc_final: 0.7382 (tp40)
  outliers start: 6
  outliers final: 5
  residues processed: 101
  average time/residue: 0.4179
  time to fit residues: 53.2098
Evaluate side-chains
  88 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.114518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.095080 restraints weight = 27676.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099934 restraints weight = 10641.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102954 restraints weight = 5528.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5491  Z= 0.271
  Angle     :  0.710   6.492   7484  Z= 0.365
  Chirality :  0.042   0.200    854
  Planarity :  0.005   0.055    935
  Dihedral  : 10.680  62.539   1180
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.08 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.52 (0.33), residues: 614
  helix:  0.83 (0.25), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.32 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 552 
 HIS   0.011   0.002   HIS A 251 
 PHE   0.016   0.002   PHE A 294 
 TYR   0.019   0.002   TYR A 215 
 ARG   0.004   0.000   ARG A 381 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.776 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8897 (tpt170) cc_final: 0.8670 (ttp-110)
REVERT: A   91 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6192 (tt)
REVERT: A  132 LYS cc_start: 0.8205 (tttt) cc_final: 0.7947 (mmpt)
REVERT: A  182 SER cc_start: 0.9085 (t) cc_final: 0.8734 (m)
REVERT: A  183 ASN cc_start: 0.8352 (m-40) cc_final: 0.7779 (t0)
REVERT: A  215 TYR cc_start: 0.6711 (t80) cc_final: 0.6386 (t80)
REVERT: A  309 MET cc_start: 0.9035 (mmp) cc_final: 0.8803 (mmp)
REVERT: A  338 TYR cc_start: 0.9225 (m-80) cc_final: 0.8948 (m-10)
REVERT: A  350 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7348 (ttm170)
REVERT: A  379 LEU cc_start: 0.8144 (mt) cc_final: 0.7869 (mt)
REVERT: A  453 ARG cc_start: 0.7405 (mtt90) cc_final: 0.6934 (tmm160)
REVERT: A  462 ASP cc_start: 0.8031 (m-30) cc_final: 0.7334 (t70)
REVERT: A  582 GLN cc_start: 0.7845 (mt0) cc_final: 0.7376 (tp40)
  outliers start: 8
  outliers final: 6
  residues processed: 91
  average time/residue: 0.4611
  time to fit residues: 51.9816
Evaluate side-chains
  84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.115389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.095559 restraints weight = 28130.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.100184 restraints weight = 11054.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.103114 restraints weight = 5814.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5491  Z= 0.198
  Angle     :  0.626   5.721   7484  Z= 0.321
  Chirality :  0.039   0.183    854
  Planarity :  0.004   0.056    935
  Dihedral  :  8.544  59.879   1180
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.64 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.84 (0.34), residues: 614
  helix:  1.03 (0.26), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.07 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 552 
 HIS   0.010   0.001   HIS A 251 
 PHE   0.012   0.002   PHE A 178 
 TYR   0.014   0.002   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.751 
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: 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   91 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6702 (tt)
REVERT: A  156 LEU cc_start: 0.9096 (tp) cc_final: 0.8798 (tp)
REVERT: A  182 SER cc_start: 0.9130 (t) cc_final: 0.8887 (m)
REVERT: A  183 ASN cc_start: 0.8442 (m-40) cc_final: 0.8200 (t0)
REVERT: A  215 TYR cc_start: 0.7140 (t80) cc_final: 0.6835 (t80)
REVERT: A  338 TYR cc_start: 0.9160 (m-80) cc_final: 0.8914 (m-10)
REVERT: A  350 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7402 (ttm170)
REVERT: A  453 ARG cc_start: 0.7431 (mtt90) cc_final: 0.7065 (tmm160)
REVERT: A  462 ASP cc_start: 0.8131 (m-30) cc_final: 0.7432 (t0)
REVERT: A  582 GLN cc_start: 0.8130 (mt0) cc_final: 0.7666 (tp40)
  outliers start: 12
  outliers final: 7
  residues processed: 91
  average time/residue: 0.4263
  time to fit residues: 48.7883
Evaluate side-chains
  79 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.114327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.094170 restraints weight = 28625.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.098754 restraints weight = 11389.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.101702 restraints weight = 6055.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5491  Z= 0.277
  Angle     :  0.641   5.852   7484  Z= 0.332
  Chirality :  0.039   0.188    854
  Planarity :  0.004   0.050    935
  Dihedral  :  7.970  59.293   1180
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.02 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.63 (0.34), residues: 614
  helix:  0.90 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.24 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 552 
 HIS   0.009   0.002   HIS A 251 
 PHE   0.016   0.001   PHE A 509 
 TYR   0.017   0.002   TYR A 215 
 ARG   0.003   0.000   ARG A 380 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.708 
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: 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: symmetry clash
   revert: symmetry clash
REVERT: A  182 SER cc_start: 0.9103 (t) cc_final: 0.8851 (m)
REVERT: A  183 ASN cc_start: 0.8481 (m-40) cc_final: 0.8207 (t0)
REVERT: A  215 TYR cc_start: 0.7254 (t80) cc_final: 0.6970 (t80)
REVERT: A  341 LYS cc_start: 0.7836 (mttt) cc_final: 0.7457 (mmmt)
REVERT: A  350 ARG cc_start: 0.7732 (ttt180) cc_final: 0.7444 (ttm170)
REVERT: A  453 ARG cc_start: 0.7430 (mtt90) cc_final: 0.6990 (tmm160)
REVERT: A  462 ASP cc_start: 0.8146 (m-30) cc_final: 0.7877 (t0)
REVERT: A  582 GLN cc_start: 0.8164 (mt0) cc_final: 0.7654 (tp40)
  outliers start: 10
  outliers final: 8
  residues processed: 82
  average time/residue: 0.4157
  time to fit residues: 43.6006
Evaluate side-chains
  76 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0070
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.116353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.096095 restraints weight = 28303.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.100813 restraints weight = 11099.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.103798 restraints weight = 5844.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5491  Z= 0.169
  Angle     :  0.584   5.448   7484  Z= 0.297
  Chirality :  0.037   0.196    854
  Planarity :  0.004   0.034    935
  Dihedral  :  7.317  58.904   1180
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.53 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.91 (0.34), residues: 614
  helix:  1.12 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.12 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 552 
 HIS   0.010   0.001   HIS A 251 
 PHE   0.011   0.001   PHE A 178 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 380 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.863 
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: 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  156 LEU cc_start: 0.9055 (tp) cc_final: 0.8756 (tp)
REVERT: A  182 SER cc_start: 0.9123 (t) cc_final: 0.8878 (m)
REVERT: A  183 ASN cc_start: 0.8477 (m-40) cc_final: 0.8250 (t0)
REVERT: A  215 TYR cc_start: 0.6987 (t80) cc_final: 0.6703 (t80)
REVERT: A  341 LYS cc_start: 0.7793 (mttt) cc_final: 0.7409 (mmmt)
REVERT: A  350 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7376 (ttm170)
REVERT: A  453 ARG cc_start: 0.7394 (mtt90) cc_final: 0.6881 (tmm160)
REVERT: A  582 GLN cc_start: 0.8155 (mt0) cc_final: 0.7814 (mm110)
  outliers start: 9
  outliers final: 8
  residues processed: 81
  average time/residue: 0.3937
  time to fit residues: 40.8425
Evaluate side-chains
  76 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.113777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.095524 restraints weight = 27349.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.099983 restraints weight = 10186.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.102869 restraints weight = 5169.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5491  Z= 0.236
  Angle     :  0.598   6.162   7484  Z= 0.308
  Chirality :  0.038   0.182    854
  Planarity :  0.004   0.033    935
  Dihedral  :  7.095  58.414   1180
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.34 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.84 (0.34), residues: 614
  helix:  1.12 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.27 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.008   0.001   HIS A 251 
 PHE   0.020   0.002   PHE A 511 
 TYR   0.015   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.767 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 SER cc_start: 0.9135 (t) cc_final: 0.8875 (m)
REVERT: A  183 ASN cc_start: 0.8450 (m-40) cc_final: 0.8210 (t0)
REVERT: A  215 TYR cc_start: 0.7160 (t80) cc_final: 0.6867 (t80)
REVERT: A  341 LYS cc_start: 0.7873 (mttt) cc_final: 0.7523 (mmmt)
REVERT: A  453 ARG cc_start: 0.7429 (mtt90) cc_final: 0.6799 (tmm160)
REVERT: A  529 ASP cc_start: 0.8559 (p0) cc_final: 0.8335 (p0)
REVERT: A  582 GLN cc_start: 0.8204 (mt0) cc_final: 0.7858 (mm110)
REVERT: A  599 TRP cc_start: 0.8227 (t60) cc_final: 0.7682 (t60)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.4145
  time to fit residues: 40.2715
Evaluate side-chains
  75 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.089293 restraints weight = 28314.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.094064 restraints weight = 10172.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.097067 restraints weight = 5082.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5491  Z= 0.358
  Angle     :  0.657   5.924   7484  Z= 0.344
  Chirality :  0.040   0.204    854
  Planarity :  0.004   0.034    935
  Dihedral  :  7.302  57.395   1180
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.34 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.33 (0.33), residues: 614
  helix:  0.78 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.62 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  40 
 HIS   0.008   0.002   HIS A 251 
 PHE   0.022   0.002   PHE A 511 
 TYR   0.019   0.002   TYR A 215 
 ARG   0.006   0.000   ARG A 381 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.746 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 SER cc_start: 0.9144 (t) cc_final: 0.8757 (m)
REVERT: A  183 ASN cc_start: 0.8454 (m-40) cc_final: 0.8246 (t0)
REVERT: A  215 TYR cc_start: 0.6947 (t80) cc_final: 0.6628 (t80)
REVERT: A  341 LYS cc_start: 0.8218 (mttt) cc_final: 0.7876 (mmpt)
REVERT: A  350 ARG cc_start: 0.7860 (ttm170) cc_final: 0.6943 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7367 (mtt90) cc_final: 0.6532 (tmm160)
REVERT: A  582 GLN cc_start: 0.8072 (mt0) cc_final: 0.7718 (mm110)
  outliers start: 9
  outliers final: 9
  residues processed: 77
  average time/residue: 0.4118
  time to fit residues: 40.1983
Evaluate side-chains
  78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.112947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092149 restraints weight = 29028.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.097177 restraints weight = 11047.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.100451 restraints weight = 5744.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5491  Z= 0.179
  Angle     :  0.578   6.338   7484  Z= 0.298
  Chirality :  0.037   0.211    854
  Planarity :  0.004   0.034    935
  Dihedral  :  6.845  57.856   1180
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.91 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.80 (0.34), residues: 614
  helix:  1.11 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.34 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 552 
 HIS   0.008   0.001   HIS A 251 
 PHE   0.017   0.002   PHE A 511 
 TYR   0.012   0.001   TYR A 175 
 ARG   0.003   0.000   ARG A 479 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.848 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 LEU cc_start: 0.8892 (tp) cc_final: 0.8614 (tp)
REVERT: A  182 SER cc_start: 0.9086 (t) cc_final: 0.8723 (m)
REVERT: A  183 ASN cc_start: 0.8449 (m-40) cc_final: 0.8219 (t0)
REVERT: A  341 LYS cc_start: 0.8077 (mttt) cc_final: 0.7747 (mmpt)
REVERT: A  350 ARG cc_start: 0.7738 (ttm170) cc_final: 0.6804 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7400 (mtt90) cc_final: 0.6542 (tmm160)
REVERT: A  582 GLN cc_start: 0.7957 (mt0) cc_final: 0.7615 (mm110)
REVERT: A  599 TRP cc_start: 0.8011 (t60) cc_final: 0.7437 (t60)
  outliers start: 9
  outliers final: 8
  residues processed: 72
  average time/residue: 0.4740
  time to fit residues: 42.7762
Evaluate side-chains
  72 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.113563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.092769 restraints weight = 28886.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097818 restraints weight = 11058.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101072 restraints weight = 5752.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5491  Z= 0.181
  Angle     :  0.567   6.302   7484  Z= 0.294
  Chirality :  0.036   0.202    854
  Planarity :  0.004   0.034    935
  Dihedral  :  6.546  57.565   1180
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.28 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.01 (0.35), residues: 614
  helix:  1.29 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.26 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 552 
 HIS   0.006   0.001   HIS A 251 
 PHE   0.019   0.001   PHE A 511 
 TYR   0.013   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 380 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.757 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7034 (ttt90)
REVERT: A  110 GLN cc_start: 0.7928 (tt0) cc_final: 0.7650 (tp40)
REVERT: A  182 SER cc_start: 0.9090 (t) cc_final: 0.8725 (m)
REVERT: A  183 ASN cc_start: 0.8464 (m-40) cc_final: 0.8227 (t0)
REVERT: A  341 LYS cc_start: 0.8072 (mttt) cc_final: 0.7751 (mmpt)
REVERT: A  350 ARG cc_start: 0.7782 (ttm170) cc_final: 0.6923 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7404 (mtt90) cc_final: 0.6542 (tmm160)
REVERT: A  582 GLN cc_start: 0.7921 (mt0) cc_final: 0.7361 (tp40)
REVERT: A  599 TRP cc_start: 0.8042 (t60) cc_final: 0.7438 (t60)
  outliers start: 7
  outliers final: 7
  residues processed: 70
  average time/residue: 0.4442
  time to fit residues: 39.1515
Evaluate side-chains
  72 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   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 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.113625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.092837 restraints weight = 29023.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.097873 restraints weight = 11098.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.101163 restraints weight = 5782.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.4853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5491  Z= 0.186
  Angle     :  0.557   6.460   7484  Z= 0.289
  Chirality :  0.036   0.200    854
  Planarity :  0.004   0.033    935
  Dihedral  :  6.318  57.270   1180
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.47 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.06 (0.35), residues: 614
  helix:  1.35 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.28 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.006   0.001   HIS A 251 
 PHE   0.024   0.002   PHE A 509 
 TYR   0.013   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3485.80 seconds
wall clock time: 62 minutes 14.90 seconds (3734.90 seconds total)