Starting phenix.real_space_refine
on Sat May  2 12:45:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9udc_64067/05_2026/9udc_64067.map"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.067
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      29      5.16       5
     C    3434      2.51       5
     N     850      2.21       5
     O     935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5250
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 657, 5206
          Classifications: {'peptide': 657}
          Link IDs: {'PTRANS': 24, 'TRANS': 632}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.43, per 1000 atoms: 0.27
  Number of scatterers: 5250
  At special positions: 0
  Unit cell: (82.29, 87.565, 124.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P       2     15.00
     O     935      8.00
     N     850      7.00
     C    3434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 158.8 milliseconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1234

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 7 sheets defined
      58.9% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 4.178A  pdb=" N   ILE A  46 " --> pdb=" O   TYR A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 66
      removed outlier: 4.038A  pdb=" N   VAL A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 74
    Processing helix  chain 'A' and resid 78 through 109
      removed outlier: 3.705A  pdb=" N   THR A  96 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 3.770A  pdb=" N   ALA A 102 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TRP A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 132
    Processing helix  chain 'A' and resid 138 through 172
      Proline residue:  A 162  - end of helix
      removed outlier: 4.652A  pdb=" N   ALA A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 209
      Proline residue:  A 203  - end of helix
      removed outlier: 3.859A  pdb=" N   VAL A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 238
      removed outlier: 3.971A  pdb=" N   ALA A 220 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      Proline residue:  A 224  - end of helix
      removed outlier: 3.788A  pdb=" N   GLY A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 270
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 289 through 304
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 308 through 317
      removed outlier: 4.144A  pdb=" N   PHE A 312 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TRP A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 315 " --> pdb=" O   MET A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 329
      removed outlier: 4.095A  pdb=" N   ARG A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 346 through 354
    Processing helix  chain 'A' and resid 355 through 362
    Processing helix  chain 'A' and resid 362 through 370
    Processing helix  chain 'A' and resid 371 through 375
      removed outlier: 4.024A  pdb=" N   SER A 375 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 405
      removed outlier: 3.598A  pdb=" N   PHE A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 610
    Processing helix  chain 'A' and resid 611 through 637
      removed outlier: 4.345A  pdb=" N   VAL A 627 " --> pdb=" O   VAL A 623 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   THR A 628 " --> pdb=" O   MET A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 667
      removed outlier: 3.642A  pdb=" N   ILE A 653 " --> pdb=" O   TRP A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 695
      removed outlier: 3.912A  pdb=" N   TYR A 695 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 456
      removed outlier: 7.453A  pdb=" N   GLU A 413 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   TYR A 487 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE A 415 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   LEU A 489 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE A 491 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU A 419 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   GLU A 493 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 456
      removed outlier: 7.453A  pdb=" N   GLU A 413 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   TYR A 487 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE A 415 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   LEU A 489 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE A 491 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU A 419 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   GLU A 493 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443
    Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 517
    Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.837A  pdb=" N   GLY A 544 " --> pdb=" O   ASN A 521 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASN A 521 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU A 582 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE A 598 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 584 " --> pdb=" O   TRP A 596 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 536 through 539
      removed outlier: 3.688A  pdb=" N   VAL A 527 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   HIS A 560 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555
      removed outlier: 3.971A  pdb=" N   GLY A 554 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 817
        1.31 -     1.44: 1514
        1.44 -     1.56: 2998
        1.56 -     1.68: 10
        1.68 -     1.81: 47
  Bond restraints: 5386
  Sorted by residual:
  bond pdb=" C3D NAD A 801 "
       pdb=" C4D NAD A 801 "
    ideal  model  delta    sigma   weight residual
    1.531  1.281  0.250 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C4D NAD A 801 "
       pdb=" O4D NAD A 801 "
    ideal  model  delta    sigma   weight residual
    1.445  1.679 -0.234 2.00e-02 2.50e+03 1.37e+02
  bond pdb=" C2B NAD A 801 "
       pdb=" C3B NAD A 801 "
    ideal  model  delta    sigma   weight residual
    1.524  1.337  0.187 2.00e-02 2.50e+03 8.76e+01
  bond pdb=" C1B NAD A 801 "
       pdb=" O4B NAD A 801 "
    ideal  model  delta    sigma   weight residual
    1.402  1.587 -0.185 2.00e-02 2.50e+03 8.56e+01
  bond pdb=" C6A NAD A 801 "
       pdb=" N6A NAD A 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.472 -0.138 2.00e-02 2.50e+03 4.77e+01
  ... (remaining 5381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 7231
        2.58 -     5.16: 75
        5.16 -     7.74: 17
        7.74 -    10.32: 3
       10.32 -    12.90: 3
  Bond angle restraints: 7329
  Sorted by residual:
  angle pdb=" C   SER A 375 "
        pdb=" CA  SER A 375 "
        pdb=" CB  SER A 375 "
      ideal   model   delta    sigma   weight residual
     116.54  109.93    6.61 1.15e+00 7.56e-01 3.30e+01
  angle pdb=" CA  PRO A 134 "
        pdb=" N   PRO A 134 "
        pdb=" CD  PRO A 134 "
      ideal   model   delta    sigma   weight residual
     112.00  104.60    7.40 1.40e+00 5.10e-01 2.79e+01
  angle pdb=" O1A NAD A 801 "
        pdb=" PA  NAD A 801 "
        pdb=" O2A NAD A 801 "
      ideal   model   delta    sigma   weight residual
     122.64  109.74   12.90 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" O3  NAD A 801 "
        pdb=" PN  NAD A 801 "
        pdb=" O5D NAD A 801 "
      ideal   model   delta    sigma   weight residual
      98.00  109.98  -11.98 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" O1N NAD A 801 "
        pdb=" PN  NAD A 801 "
        pdb=" O2N NAD A 801 "
      ideal   model   delta    sigma   weight residual
     120.02  109.07   10.95 3.00e+00 1.11e-01 1.33e+01
  ... (remaining 7324 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 2711
       15.83 -    31.65: 313
       31.65 -    47.48: 104
       47.48 -    63.30: 30
       63.30 -    79.13: 23
  Dihedral angle restraints: 3181
    sinusoidal: 1262
      harmonic: 1919
  Sorted by residual:
  dihedral pdb=" CA  PHE A 625 "
           pdb=" C   PHE A 625 "
           pdb=" N   SER A 626 "
           pdb=" CA  SER A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CG  ARG A 332 "
           pdb=" CD  ARG A 332 "
           pdb=" NE  ARG A 332 "
           pdb=" CZ  ARG A 332 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.11  -44.89     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CA  GLN A 636 "
           pdb=" CB  GLN A 636 "
           pdb=" CG  GLN A 636 "
           pdb=" CD  GLN A 636 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.44  -57.56     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 3178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 710
       0.058 -    0.117: 122
       0.117 -    0.175: 4
       0.175 -    0.234: 1
       0.234 -    0.292: 1
  Chirality restraints: 838
  Sorted by residual:
  chirality pdb=" C3D NAD A 801 "
            pdb=" C2D NAD A 801 "
            pdb=" C4D NAD A 801 "
            pdb=" O3D NAD A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.44   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" C3B NAD A 801 "
            pdb=" C2B NAD A 801 "
            pdb=" C4B NAD A 801 "
            pdb=" O3B NAD A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.49   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C1B NAD A 801 "
            pdb=" C2B NAD A 801 "
            pdb=" N9A NAD A 801 "
            pdb=" O4B NAD A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.50   -0.15 2.00e-01 2.50e+01 5.90e-01
  ... (remaining 835 not shown)

  Planarity restraints: 906
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 133 "    0.043 5.00e-02 4.00e+02   6.24e-02 6.24e+00
        pdb=" N   PRO A 134 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 134 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 134 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 121 "   -0.016 2.00e-02 2.50e+03   1.15e-02 2.66e+00
        pdb=" CG  TYR A 121 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 121 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 121 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 121 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 121 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 121 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 121 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 637 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A 638 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "    0.019 5.00e-02 4.00e+02
  ... (remaining 903 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1285
        2.79 -     3.32: 5049
        3.32 -     3.85: 8942
        3.85 -     4.37: 10070
        4.37 -     4.90: 17687
  Nonbonded interactions: 43033
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 326 "
            pdb=" NE2 GLN A 611 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OE2 GLU A 507 "
            pdb=" OG1 THR A 510 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A  70 "
            pdb=" OG  SER A 146 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OD2 ASP A 317 "
            pdb=" ND2 ASN A 657 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" OE2 GLU A 425 "
            pdb=" OG  SER A 442 "
     model   vdw
     2.319 3.040
  ... (remaining 43028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.420
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
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   0.250   5387  Z= 0.413
  Angle     :  0.733  12.899   7329  Z= 0.368
  Chirality :  0.043   0.292    838
  Planarity :  0.004   0.062    906
  Dihedral  : 17.429  79.126   1947
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.21 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.33), residues: 655
  helix:  1.20 (0.28), residues: 354
  sheet:  0.20 (0.46), residues: 106
  loop : -1.14 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 206 
 TYR   0.028   0.001   TYR A 121 
 PHE   0.017   0.001   PHE A 625 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.006   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00849 ( 5386)
  covalent geometry    : angle       0.73254 ( 7329)
  hydrogen bonds       : bond        0.12572 (  316)
  hydrogen bonds       : angle       6.72140 (  930)
  Misc. bond           : bond        0.00121 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.179 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0472
  time to fit residues: 2.7094
Evaluate side-chains
  34 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   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 521 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.246421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.213901 restraints weight = 4631.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 0.88
r_work: 0.3632 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5387  Z= 0.152
  Angle     :  0.575   8.045   7329  Z= 0.290
  Chirality :  0.042   0.134    838
  Planarity :  0.004   0.031    906
  Dihedral  : 11.430  79.992    759
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.80 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.33), residues: 655
  helix:  1.21 (0.28), residues: 354
  sheet:  0.57 (0.50), residues: 90
  loop : -1.15 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.025   0.001   TYR A 121 
 PHE   0.014   0.001   PHE A 625 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5386)
  covalent geometry    : angle       0.57456 ( 7329)
  hydrogen bonds       : bond        0.04240 (  316)
  hydrogen bonds       : angle       5.09361 (  930)
  Misc. bond           : bond        0.00073 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  105 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.5899 (t0)
REVERT: A  317 ASP cc_start: 0.7455 (m-30) cc_final: 0.7053 (m-30)
  outliers start: 10
  outliers final: 2
  residues processed: 48
  average time/residue: 0.0427
  time to fit residues: 3.2342
Evaluate side-chains
  41 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  545 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4345 r_free = 0.4345 target = 0.219087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.161684 restraints weight = 4915.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.08
r_work: 0.3236 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5387  Z= 0.198
  Angle     :  0.597   8.627   7329  Z= 0.302
  Chirality :  0.043   0.139    838
  Planarity :  0.004   0.036    906
  Dihedral  : 10.071  85.155    759
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.98 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.33), residues: 655
  helix:  0.98 (0.27), residues: 358
  sheet:  0.66 (0.51), residues: 90
  loop : -1.09 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 322 
 TYR   0.023   0.002   TYR A 121 
 PHE   0.014   0.002   PHE A  58 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 5386)
  covalent geometry    : angle       0.59659 ( 7329)
  hydrogen bonds       : bond        0.04574 (  316)
  hydrogen bonds       : angle       4.88132 (  930)
  Misc. bond           : bond        0.00123 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  105 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6679 (t0)
REVERT: A  127 ILE cc_start: 0.8155 (mm) cc_final: 0.7898 (mt)
REVERT: A  212 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4044 (p90)
REVERT: A  317 ASP cc_start: 0.7799 (m-30) cc_final: 0.7418 (m-30)
REVERT: A  581 TYR cc_start: 0.7272 (m-80) cc_final: 0.6793 (m-80)
REVERT: A  606 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6340 (ttm)
REVERT: A  694 TYR cc_start: 0.7794 (t80) cc_final: 0.7551 (t80)
  outliers start: 15
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0494
  time to fit residues: 3.9053
Evaluate side-chains
  49 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  697 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 49 optimal weight:   40.0000
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4692 r_free = 0.4692 target = 0.244729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 112)---------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.199423 restraints weight = 4632.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 0.88
r_work: 0.3518 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5387  Z= 0.150
  Angle     :  0.543   8.171   7329  Z= 0.277
  Chirality :  0.041   0.135    838
  Planarity :  0.003   0.038    906
  Dihedral  :  9.766  89.734    759
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.04 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.33), residues: 655
  helix:  1.18 (0.28), residues: 354
  sheet:  0.52 (0.50), residues: 93
  loop : -1.09 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 518 
 TYR   0.017   0.001   TYR A 121 
 PHE   0.010   0.001   PHE A 187 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.006   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5386)
  covalent geometry    : angle       0.54330 ( 7329)
  hydrogen bonds       : bond        0.04004 (  316)
  hydrogen bonds       : angle       4.64618 (  930)
  Misc. bond           : bond        0.00087 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ILE cc_start: 0.8241 (mm) cc_final: 0.7978 (mt)
REVERT: A  212 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.3929 (p90)
REVERT: A  302 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8216 (p)
REVERT: A  317 ASP cc_start: 0.7499 (m-30) cc_final: 0.7139 (m-30)
REVERT: A  404 MET cc_start: 0.8518 (ttm) cc_final: 0.8172 (ttm)
REVERT: A  581 TYR cc_start: 0.7363 (m-80) cc_final: 0.6854 (m-80)
  outliers start: 11
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0597
  time to fit residues: 4.1824
Evaluate side-chains
  47 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  545 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0070
   chunk 16 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0060
   chunk 57 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.3814

-------------------------------------------------------------------------------
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 = 0.4386 r_free = 0.4386 target = 0.224151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.170606 restraints weight = 4995.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.26
r_work: 0.3307 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5387  Z= 0.112
  Angle     :  0.507   7.768   7329  Z= 0.259
  Chirality :  0.040   0.133    838
  Planarity :  0.003   0.036    906
  Dihedral  :  9.446  89.803    759
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.39 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.33), residues: 655
  helix:  1.39 (0.28), residues: 354
  sheet:  0.44 (0.50), residues: 93
  loop : -1.03 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.013   0.001   TYR A 121 
 PHE   0.011   0.001   PHE A 187 
 TRP   0.007   0.001   TRP A 649 
 HIS   0.006   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5386)
  covalent geometry    : angle       0.50676 ( 7329)
  hydrogen bonds       : bond        0.03516 (  316)
  hydrogen bonds       : angle       4.42121 (  930)
  Misc. bond           : bond        0.00061 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.3791 (p90)
REVERT: A  302 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (p)
REVERT: A  317 ASP cc_start: 0.7410 (m-30) cc_final: 0.7030 (m-30)
REVERT: A  502 MET cc_start: 0.7523 (tpp) cc_final: 0.7313 (tpp)
REVERT: A  606 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6031 (ttm)
  outliers start: 14
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0467
  time to fit residues: 3.5764
Evaluate side-chains
  48 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  669 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0030
   chunk 46 optimal weight:    0.0570
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 48 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0770
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.1866

-------------------------------------------------------------------------------
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 = 0.4732 r_free = 0.4732 target = 0.251037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 188)---------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.205722 restraints weight = 4663.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 0.80
r_work: 0.3588 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 2.31 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5387  Z= 0.095
  Angle     :  0.483   7.240   7329  Z= 0.245
  Chirality :  0.039   0.128    838
  Planarity :  0.003   0.033    906
  Dihedral  :  9.020  88.020    759
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.09 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.33), residues: 655
  helix:  1.63 (0.28), residues: 354
  sheet:  0.49 (0.48), residues: 95
  loop : -1.02 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.010   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 187 
 TRP   0.007   0.001   TRP A 649 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 5386)
  covalent geometry    : angle       0.48255 ( 7329)
  hydrogen bonds       : bond        0.03198 (  316)
  hydrogen bonds       : angle       4.20107 (  930)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7963 (p)
REVERT: A  317 ASP cc_start: 0.7275 (m-30) cc_final: 0.6989 (m-30)
REVERT: A  502 MET cc_start: 0.7585 (tpp) cc_final: 0.7042 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0756
  time to fit residues: 5.4900
Evaluate side-chains
  49 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 52 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 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 = 0.4340 r_free = 0.4340 target = 0.219235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.162065 restraints weight = 4953.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.32
r_work: 0.3223 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5387  Z= 0.189
  Angle     :  0.575   8.559   7329  Z= 0.290
  Chirality :  0.043   0.139    838
  Planarity :  0.003   0.036    906
  Dihedral  :  9.474  89.880    759
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.91 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.33), residues: 655
  helix:  1.24 (0.28), residues: 355
  sheet:  0.56 (0.49), residues: 95
  loop : -0.99 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 180 
 TYR   0.017   0.002   TYR A 121 
 PHE   0.013   0.001   PHE A  58 
 TRP   0.011   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 5386)
  covalent geometry    : angle       0.57530 ( 7329)
  hydrogen bonds       : bond        0.04290 (  316)
  hydrogen bonds       : angle       4.46478 (  930)
  Misc. bond           : bond        0.00150 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ILE cc_start: 0.8234 (mm) cc_final: 0.7997 (mt)
REVERT: A  317 ASP cc_start: 0.7585 (m-30) cc_final: 0.7238 (m-30)
REVERT: A  502 MET cc_start: 0.7595 (tpp) cc_final: 0.7173 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0551
  time to fit residues: 4.1950
Evaluate side-chains
  49 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  635 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 41 optimal weight:    9.9990
   chunk 58 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0470
   chunk 13 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.4078

-------------------------------------------------------------------------------
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 = 0.4394 r_free = 0.4394 target = 0.224174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.169224 restraints weight = 4808.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.99
r_work: 0.3317 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5387  Z= 0.112
  Angle     :  0.506   7.898   7329  Z= 0.255
  Chirality :  0.040   0.128    838
  Planarity :  0.003   0.036    906
  Dihedral  :  9.247  89.778    759
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.44 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.33), residues: 655
  helix:  1.48 (0.28), residues: 355
  sheet:  0.57 (0.49), residues: 95
  loop : -0.96 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.013   0.001   TYR A 121 
 PHE   0.011   0.001   PHE A 187 
 TRP   0.007   0.001   TRP A 672 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5386)
  covalent geometry    : angle       0.50631 ( 7329)
  hydrogen bonds       : bond        0.03532 (  316)
  hydrogen bonds       : angle       4.26227 (  930)
  Misc. bond           : bond        0.00048 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 ILE cc_start: 0.8223 (mm) cc_final: 0.7998 (mt)
REVERT: A  302 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8218 (p)
REVERT: A  317 ASP cc_start: 0.7529 (m-30) cc_final: 0.7188 (m-30)
REVERT: A  330 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9019 (mtm)
REVERT: A  502 MET cc_start: 0.7521 (tpp) cc_final: 0.7200 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0557
  time to fit residues: 4.1291
Evaluate side-chains
  53 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  690 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4678 r_free = 0.4678 target = 0.244119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.218385 restraints weight = 4706.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 0.66
r_work: 0.3679 rms_B_bonded: 0.99 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5387  Z= 0.171
  Angle     :  0.556   8.386   7329  Z= 0.280
  Chirality :  0.042   0.134    838
  Planarity :  0.003   0.039    906
  Dihedral  :  9.414  89.734    759
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.27 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.33), residues: 655
  helix:  1.32 (0.28), residues: 355
  sheet:  0.51 (0.48), residues: 95
  loop : -1.01 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 182 
 TYR   0.016   0.002   TYR A  86 
 PHE   0.011   0.001   PHE A 187 
 TRP   0.011   0.001   TRP A 280 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 5386)
  covalent geometry    : angle       0.55583 ( 7329)
  hydrogen bonds       : bond        0.04102 (  316)
  hydrogen bonds       : angle       4.35723 (  930)
  Misc. bond           : bond        0.00126 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6395 (t0)
REVERT: A  317 ASP cc_start: 0.7256 (m-30) cc_final: 0.6955 (m-30)
REVERT: A  330 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9138 (mtm)
REVERT: A  502 MET cc_start: 0.7349 (tpp) cc_final: 0.7077 (mmm)
REVERT: A  641 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6760 (mtp)
  outliers start: 14
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0506
  time to fit residues: 3.8940
Evaluate side-chains
  53 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  690 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 23 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0060
   chunk 27 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.3914

-------------------------------------------------------------------------------
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 = 0.4376 r_free = 0.4376 target = 0.223664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.166430 restraints weight = 4883.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.12
r_work: 0.3281 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5387  Z= 0.111
  Angle     :  0.505   7.829   7329  Z= 0.256
  Chirality :  0.040   0.127    838
  Planarity :  0.003   0.037    906
  Dihedral  :  9.199  89.637    759
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.14 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.33), residues: 655
  helix:  1.49 (0.28), residues: 355
  sheet:  0.50 (0.48), residues: 95
  loop : -0.95 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 518 
 TYR   0.012   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 187 
 TRP   0.009   0.001   TRP A 260 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5386)
  covalent geometry    : angle       0.50452 ( 7329)
  hydrogen bonds       : bond        0.03510 (  316)
  hydrogen bonds       : angle       4.17572 (  930)
  Misc. bond           : bond        0.00043 (    1)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6604 (t0)
REVERT: A  302 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8198 (p)
REVERT: A  317 ASP cc_start: 0.7595 (m-30) cc_final: 0.7258 (m-30)
REVERT: A  330 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9009 (mtm)
REVERT: A  502 MET cc_start: 0.7320 (tpp) cc_final: 0.7014 (mmm)
REVERT: A  641 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6931 (mtp)
  outliers start: 12
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0689
  time to fit residues: 4.6961
Evaluate side-chains
  52 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  641 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0070
   chunk 42 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 38 optimal weight:   30.0000
   chunk 36 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.4695 r_free = 0.4695 target = 0.246363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 164)---------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.206375 restraints weight = 4622.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 0.73
r_work: 0.3570 rms_B_bonded: 1.18 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 2.27 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5387  Z= 0.121
  Angle     :  0.519   7.978   7329  Z= 0.263
  Chirality :  0.041   0.128    838
  Planarity :  0.003   0.038    906
  Dihedral  :  9.139  89.871    759
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.97 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.33), residues: 655
  helix:  1.54 (0.28), residues: 355
  sheet:  0.60 (0.47), residues: 97
  loop : -0.96 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 206 
 TYR   0.012   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 187 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5386)
  covalent geometry    : angle       0.51917 ( 7329)
  hydrogen bonds       : bond        0.03607 (  316)
  hydrogen bonds       : angle       4.15880 (  930)
  Misc. bond           : bond        0.00079 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.44 seconds
wall clock time: 27 minutes 25.74 seconds (1645.74 seconds total)