Starting phenix.real_space_refine
on Tue Mar  3 13:51:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10kr_75254/03_2026/10kr_75254.map"
  }
  resolution = 3.57
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3370      2.51       5
     N     990      2.21       5
     O    1020      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5400
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 540
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
  Restraints were copied for chains:
    E, B, D, C, F, J, G, I, H
  Time building chain proxies: 0.50, per 1000 atoms: 0.09
  Number of scatterers: 5400
  At special positions: 0
  Unit cell: (81, 178.2, 49.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1020      8.00
     N     990      7.00
     C    3370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 289.0 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 36.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 308 through 310
      removed outlier: 6.781A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314
      removed outlier: 7.300A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 320
      removed outlier: 6.686A  pdb=" N   LYS A 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   SER D 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   THR A 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 336 through 345
      removed outlier: 6.930A  pdb=" N   LEU D 344 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASP E 345 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLN A 336 " --> pdb=" O   MET D 337 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL D 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   SER D 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LYS A 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   LYS D 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   GLU A 342 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   ASP D 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 9.305A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU B 344 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ASP A 345 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU C 344 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASP B 345 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 357
      removed outlier: 6.516A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   SER D 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY A 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 360 through 362
      removed outlier: 6.882A  pdb=" N   ILE A 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 374 through 376
      removed outlier: 6.906A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'J' and resid 308 through 310
      removed outlier: 6.781A  pdb=" N   VAL F 309 " --> pdb=" O   TYR I 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 313 through 314
      removed outlier: 7.301A  pdb=" N   VAL F 313 " --> pdb=" O   ASP I 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 317 through 320
      removed outlier: 6.686A  pdb=" N   LYS F 317 " --> pdb=" O   VAL I 318 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   SER I 320 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   THR F 319 " --> pdb=" O   SER I 320 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 336 through 345
      removed outlier: 6.930A  pdb=" N   LEU I 344 " --> pdb=" O   LYS J 343 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASP J 345 " --> pdb=" O   LEU I 344 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLN F 336 " --> pdb=" O   MET I 337 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL I 339 " --> pdb=" O   GLN F 336 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   GLU F 338 " --> pdb=" O   VAL I 339 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   SER I 341 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LYS F 340 " --> pdb=" O   SER I 341 " (cutoff:3.500A)
      removed outlier: 8.504A  pdb=" N   LYS I 343 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   GLU F 342 " --> pdb=" O   LYS I 343 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   ASP I 345 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
      removed outlier: 9.305A  pdb=" N   LEU F 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU G 344 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ASP F 345 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU H 344 " --> pdb=" O   LYS G 343 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASP G 345 " --> pdb=" O   LEU H 344 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 350 through 357
      removed outlier: 6.516A  pdb=" N   GLN F 351 " --> pdb=" O   SER I 352 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   ILE I 354 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LYS F 353 " --> pdb=" O   ILE I 354 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   SER I 356 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY F 355 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 360 through 362
      removed outlier: 6.882A  pdb=" N   ILE F 360 " --> pdb=" O   THR I 361 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'J' and resid 374 through 376
      removed outlier: 6.906A  pdb=" N   LYS F 375 " --> pdb=" O   LEU I 376 " (cutoff:3.500A)

    144 hydrogen bonds defined for protein.
    432 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: 0.69

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1790
        1.34 -     1.46: 836
        1.46 -     1.58: 2824
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 5480
  Sorted by residual:
  bond pdb=" N   HIS J 374 "
       pdb=" CA  HIS J 374 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.26e-02 6.30e+03 8.57e+00
  bond pdb=" N   HIS E 374 "
       pdb=" CA  HIS E 374 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.037 1.26e-02 6.30e+03 8.49e+00
  bond pdb=" N   HIS D 374 "
       pdb=" CA  HIS D 374 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.26e-02 6.30e+03 8.32e+00
  bond pdb=" N   HIS H 374 "
       pdb=" CA  HIS H 374 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.26e-02 6.30e+03 8.28e+00
  bond pdb=" N   HIS G 374 "
       pdb=" CA  HIS G 374 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.26e-02 6.30e+03 8.23e+00
  ... (remaining 5475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 6790
        2.21 -     4.43: 451
        4.43 -     6.64: 49
        6.64 -     8.85: 10
        8.85 -    11.06: 20
  Bond angle restraints: 7320
  Sorted by residual:
  angle pdb=" CA  HIS J 374 "
        pdb=" CB  HIS J 374 "
        pdb=" CG  HIS J 374 "
      ideal   model   delta    sigma   weight residual
     113.80  118.76   -4.96 1.00e+00 1.00e+00 2.46e+01
  angle pdb=" CA  HIS E 374 "
        pdb=" CB  HIS E 374 "
        pdb=" CG  HIS E 374 "
      ideal   model   delta    sigma   weight residual
     113.80  118.76   -4.96 1.00e+00 1.00e+00 2.46e+01
  angle pdb=" CA  HIS I 374 "
        pdb=" CB  HIS I 374 "
        pdb=" CG  HIS I 374 "
      ideal   model   delta    sigma   weight residual
     113.80  118.73   -4.93 1.00e+00 1.00e+00 2.43e+01
  angle pdb=" CA  HIS D 374 "
        pdb=" CB  HIS D 374 "
        pdb=" CG  HIS D 374 "
      ideal   model   delta    sigma   weight residual
     113.80  118.72   -4.92 1.00e+00 1.00e+00 2.42e+01
  angle pdb=" CA  HIS B 374 "
        pdb=" CB  HIS B 374 "
        pdb=" CG  HIS B 374 "
      ideal   model   delta    sigma   weight residual
     113.80  118.71   -4.91 1.00e+00 1.00e+00 2.41e+01
  ... (remaining 7315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.15: 2780
       11.15 -    22.30: 340
       22.30 -    33.45: 100
       33.45 -    44.60: 100
       44.60 -    55.74: 50
  Dihedral angle restraints: 3370
    sinusoidal: 1420
      harmonic: 1950
  Sorted by residual:
  dihedral pdb=" CA  LYS B 369 "
           pdb=" C   LYS B 369 "
           pdb=" N   LYS B 370 "
           pdb=" CA  LYS B 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.67   21.33     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  LYS F 369 "
           pdb=" C   LYS F 369 "
           pdb=" N   LYS F 370 "
           pdb=" CA  LYS F 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.68   21.32     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  LYS H 369 "
           pdb=" C   LYS H 369 "
           pdb=" N   LYS H 370 "
           pdb=" CA  LYS H 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.69   21.31     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 3367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 753
       0.110 -    0.220: 47
       0.220 -    0.330: 10
       0.330 -    0.440: 0
       0.440 -    0.550: 10
  Chirality restraints: 820
  Sorted by residual:
  chirality pdb=" CB  ILE B 308 "
            pdb=" CA  ILE B 308 "
            pdb=" CG1 ILE B 308 "
            pdb=" CG2 ILE B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.09    0.55 2.00e-01 2.50e+01 7.57e+00
  chirality pdb=" CB  ILE G 308 "
            pdb=" CA  ILE G 308 "
            pdb=" CG1 ILE G 308 "
            pdb=" CG2 ILE G 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.10    0.55 2.00e-01 2.50e+01 7.51e+00
  chirality pdb=" CB  ILE A 308 "
            pdb=" CA  ILE A 308 "
            pdb=" CG1 ILE A 308 "
            pdb=" CG2 ILE A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.10    0.55 2.00e-01 2.50e+01 7.46e+00
  ... (remaining 817 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J 309 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   VAL J 309 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL J 309 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TYR J 310 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 309 "   -0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   VAL E 309 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL E 309 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TYR E 310 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 309 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.56e+00
        pdb=" C   VAL D 309 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL D 309 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TYR D 310 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1833
        2.90 -     3.40: 4228
        3.40 -     3.90: 8724
        3.90 -     4.40: 8525
        4.40 -     4.90: 16014
  Nonbonded interactions: 39324
  Sorted by model distance:
  nonbonded pdb=" OG1 THR J 361 "
            pdb=" CD2 HIS I 330 "
     model   vdw
     2.398 3.260
  nonbonded pdb=" OG1 THR E 361 "
            pdb=" CD2 HIS D 330 "
     model   vdw
     2.399 3.260
  nonbonded pdb=" OG1 THR A 361 "
            pdb=" CD2 HIS B 330 "
     model   vdw
     2.432 3.260
  nonbonded pdb=" OG1 THR F 361 "
            pdb=" CD2 HIS G 330 "
     model   vdw
     2.433 3.260
  nonbonded pdb=" OG1 THR B 361 "
            pdb=" CD2 HIS C 330 "
     model   vdw
     2.441 3.260
  ... (remaining 39319 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'C'
  selection = chain 'F'
  selection = chain 'J'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.970
  Find NCS groups from input model:        0.040
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
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      :  0.007   0.066   5480  Z= 0.431
  Angle     :  1.224  11.063   7320  Z= 0.678
  Chirality :  0.086   0.550    820
  Planarity :  0.003   0.016    930
  Dihedral  : 14.911  55.745   2130
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 33.06 %
    Favored  : 64.52 %
  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: -3.39 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG I 349 
 TYR   0.001   0.000   TYR A 310 
 PHE   0.002   0.001   PHE J 346 
 HIS   0.009   0.002   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 ( 5480)
  covalent geometry    : angle       1.22377 ( 7320)
  hydrogen bonds       : bond        0.26782 (  144)
  hydrogen bonds       : angle       7.92238 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 237
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6726 (mmtm)
REVERT: A  340 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8730 (mtpt)
REVERT: A  348 ASP cc_start: 0.8040 (t0) cc_final: 0.7607 (t0)
REVERT: A  358 ASP cc_start: 0.8809 (m-30) cc_final: 0.8516 (m-30)
REVERT: A  369 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8268 (mmmt)
REVERT: E  310 TYR cc_start: 0.4104 (t80) cc_final: 0.3806 (t80)
REVERT: E  340 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8667 (mttp)
REVERT: E  348 ASP cc_start: 0.7808 (t0) cc_final: 0.7469 (p0)
REVERT: E  358 ASP cc_start: 0.8834 (m-30) cc_final: 0.8585 (m-30)
REVERT: B  310 TYR cc_start: 0.6661 (t80) cc_final: 0.6412 (t80)
REVERT: B  317 LYS cc_start: 0.7540 (ttpt) cc_final: 0.6983 (mmtm)
REVERT: B  340 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8763 (mtpp)
REVERT: B  348 ASP cc_start: 0.7833 (t0) cc_final: 0.7551 (t0)
REVERT: D  317 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6937 (mmtm)
REVERT: D  325 LEU cc_start: 0.7715 (mt) cc_final: 0.7487 (mt)
REVERT: D  348 ASP cc_start: 0.7769 (t0) cc_final: 0.7501 (t0)
REVERT: C  317 LYS cc_start: 0.7459 (ttpt) cc_final: 0.6847 (mmtm)
REVERT: C  340 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8808 (mtpp)
REVERT: C  347 LYS cc_start: 0.6429 (mttt) cc_final: 0.6082 (mmmt)
REVERT: C  348 ASP cc_start: 0.7843 (t0) cc_final: 0.7322 (t0)
REVERT: C  358 ASP cc_start: 0.8815 (m-30) cc_final: 0.8492 (m-30)
REVERT: F  319 THR cc_start: 0.8094 (m) cc_final: 0.7724 (p)
REVERT: F  321 LYS cc_start: 0.8395 (mmtp) cc_final: 0.7797 (mmtm)
REVERT: F  324 SER cc_start: 0.9057 (m) cc_final: 0.8854 (p)
REVERT: F  348 ASP cc_start: 0.7442 (t0) cc_final: 0.6748 (m-30)
REVERT: F  349 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7231 (mmm-85)
REVERT: F  358 ASP cc_start: 0.8257 (m-30) cc_final: 0.8005 (m-30)
REVERT: F  370 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8252 (mttt)
REVERT: J  348 ASP cc_start: 0.7504 (t0) cc_final: 0.6926 (m-30)
REVERT: J  349 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7933 (mmm-85)
REVERT: J  358 ASP cc_start: 0.8265 (m-30) cc_final: 0.7997 (m-30)
REVERT: G  324 SER cc_start: 0.8620 (m) cc_final: 0.8265 (p)
REVERT: G  346 PHE cc_start: 0.8144 (m-80) cc_final: 0.7680 (m-80)
REVERT: G  348 ASP cc_start: 0.7469 (t0) cc_final: 0.6914 (m-30)
REVERT: G  349 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7328 (mmm-85)
REVERT: G  358 ASP cc_start: 0.8292 (m-30) cc_final: 0.7703 (m-30)
REVERT: I  348 ASP cc_start: 0.7345 (t0) cc_final: 0.6709 (m-30)
REVERT: I  349 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7240 (mmm-85)
REVERT: I  370 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7961 (ttmt)
REVERT: H  321 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7875 (mmtm)
REVERT: H  348 ASP cc_start: 0.7557 (t0) cc_final: 0.7119 (m-30)
REVERT: H  349 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.6925 (mmm160)
  outliers start: 15
  outliers final: 6
  residues processed: 251
  average time/residue: 0.1250
  time to fit residues: 36.6398
Evaluate side-chains
  181 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 175
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain H residue  356 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    8.9990
   overall best weight:    3.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 359 ASN
C 330 HIS
C 359 ASN
F 330 HIS
F 359 ASN
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 330 HIS
G 359 ASN
I 330 HIS
I 359 ASN
** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 330 HIS
H 359 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.131150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.089273 restraints weight = 9337.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.091774 restraints weight = 4717.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.093443 restraints weight = 3085.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.094431 restraints weight = 2357.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.094964 restraints weight = 2006.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5480  Z= 0.201
  Angle     :  0.792   7.034   7320  Z= 0.403
  Chirality :  0.051   0.253    820
  Planarity :  0.003   0.015    930
  Dihedral  :  5.854  41.390    728
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 31.13 %
    Favored  : 64.19 %
  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: -2.96 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.012   0.002   TYR B 310 
 PHE   0.009   0.002   PHE G 346 
 HIS   0.012   0.002   HIS F 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 5480)
  covalent geometry    : angle       0.79174 ( 7320)
  hydrogen bonds       : bond        0.04276 (  144)
  hydrogen bonds       : angle       5.41707 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6793 (mmtm)
REVERT: A  338 GLU cc_start: 0.7575 (mp0) cc_final: 0.7142 (mp0)
REVERT: A  340 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8580 (mtpp)
REVERT: A  342 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7590 (mp0)
REVERT: A  358 ASP cc_start: 0.8849 (m-30) cc_final: 0.8538 (m-30)
REVERT: A  374 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6762 (p-80)
REVERT: E  338 GLU cc_start: 0.8008 (mp0) cc_final: 0.7780 (mp0)
REVERT: E  340 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8772 (mtpt)
REVERT: E  343 LYS cc_start: 0.9179 (mttp) cc_final: 0.8649 (pptt)
REVERT: E  348 ASP cc_start: 0.8335 (t0) cc_final: 0.7549 (p0)
REVERT: E  358 ASP cc_start: 0.8831 (m-30) cc_final: 0.8621 (m-30)
REVERT: E  372 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8197 (mt-10)
REVERT: E  374 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5223 (m-70)
REVERT: B  317 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7093 (mmtm)
REVERT: B  340 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8328 (mtpp)
REVERT: B  342 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7092 (mp0)
REVERT: B  348 ASP cc_start: 0.8564 (t0) cc_final: 0.8230 (t0)
REVERT: D  317 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6960 (mmtm)
REVERT: D  325 LEU cc_start: 0.8039 (mt) cc_final: 0.7822 (mt)
REVERT: D  342 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7295 (mp0)
REVERT: D  348 ASP cc_start: 0.8624 (t0) cc_final: 0.8333 (t0)
REVERT: C  317 LYS cc_start: 0.7517 (ttpt) cc_final: 0.6937 (mmtm)
REVERT: C  343 LYS cc_start: 0.9023 (mttm) cc_final: 0.8766 (mttp)
REVERT: C  347 LYS cc_start: 0.7916 (mttt) cc_final: 0.7623 (mmmt)
REVERT: C  358 ASP cc_start: 0.8840 (m-30) cc_final: 0.8584 (m-30)
REVERT: F  348 ASP cc_start: 0.8332 (t0) cc_final: 0.7044 (m-30)
REVERT: F  349 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.6952 (mmm160)
REVERT: J  348 ASP cc_start: 0.8464 (t0) cc_final: 0.7483 (m-30)
REVERT: J  349 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7280 (mtm180)
REVERT: G  324 SER cc_start: 0.8225 (m) cc_final: 0.7819 (p)
REVERT: G  337 MET cc_start: 0.7832 (mpp) cc_final: 0.7488 (mmt)
REVERT: G  348 ASP cc_start: 0.8484 (t0) cc_final: 0.7456 (m-30)
REVERT: G  349 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7270 (mmm-85)
REVERT: G  358 ASP cc_start: 0.8312 (m-30) cc_final: 0.7933 (m-30)
REVERT: G  370 LYS cc_start: 0.8063 (mttt) cc_final: 0.7715 (mttp)
REVERT: I  348 ASP cc_start: 0.8459 (t0) cc_final: 0.7302 (m-30)
REVERT: I  349 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7323 (mmm-85)
REVERT: I  358 ASP cc_start: 0.8336 (m-30) cc_final: 0.8064 (m-30)
REVERT: I  369 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8464 (mtpt)
REVERT: H  348 ASP cc_start: 0.8349 (t0) cc_final: 0.7212 (m-30)
REVERT: H  349 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.6850 (mmp-170)
  outliers start: 29
  outliers final: 18
  residues processed: 201
  average time/residue: 0.1103
  time to fit residues: 26.5615
Evaluate side-chains
  199 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain E residue  374 HIS
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain J residue  356 SER
Chi-restraints excluded: chain J residue  372 GLU
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  318 VAL
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain I residue  374 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 62 optimal weight:   30.0000
   chunk 65 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:   40.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 HIS
D 330 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.124946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.083914 restraints weight = 9188.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.086227 restraints weight = 4661.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.087636 restraints weight = 3082.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.088591 restraints weight = 2413.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.088869 restraints weight = 2083.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.6193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   5480  Z= 0.298
  Angle     :  0.802   6.620   7320  Z= 0.427
  Chirality :  0.050   0.162    820
  Planarity :  0.004   0.033    930
  Dihedral  :  6.197  51.835    722
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 27.74 %
    Favored  : 66.13 %
  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: -3.18 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.016   0.002   TYR G 310 
 PHE   0.010   0.002   PHE H 346 
 HIS   0.010   0.002   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 ( 5480)
  covalent geometry    : angle       0.80206 ( 7320)
  hydrogen bonds       : bond        0.05229 (  144)
  hydrogen bonds       : angle       5.40484 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 210
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 TYR cc_start: 0.7011 (t80) cc_final: 0.6732 (t80)
REVERT: A  317 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7559 (mmtm)
REVERT: A  338 GLU cc_start: 0.7713 (mp0) cc_final: 0.7491 (mp0)
REVERT: A  340 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8603 (mtpp)
REVERT: A  342 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7638 (mp0)
REVERT: A  358 ASP cc_start: 0.8894 (m-30) cc_final: 0.8677 (m-30)
REVERT: E  340 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8704 (mtpp)
REVERT: E  343 LYS cc_start: 0.9234 (mttp) cc_final: 0.8699 (pptt)
REVERT: E  348 ASP cc_start: 0.8639 (t0) cc_final: 0.7653 (p0)
REVERT: E  374 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5413 (m-70)
REVERT: B  317 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7294 (mmtm)
REVERT: B  321 LYS cc_start: 0.8839 (mttm) cc_final: 0.8182 (ttmm)
REVERT: B  340 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8423 (mtpp)
REVERT: B  369 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9076 (mtpt)
REVERT: D  348 ASP cc_start: 0.8882 (t0) cc_final: 0.8605 (t0)
REVERT: D  372 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8318 (mt-10)
REVERT: D  375 LYS cc_start: 0.7297 (tmtt) cc_final: 0.6929 (tptt)
REVERT: C  314 ASP cc_start: 0.6510 (p0) cc_final: 0.5263 (t0)
REVERT: C  317 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7605 (mptt)
REVERT: C  321 LYS cc_start: 0.8724 (mttt) cc_final: 0.8516 (mttt)
REVERT: C  342 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7857 (mt-10)
REVERT: F  345 ASP cc_start: 0.8322 (t0) cc_final: 0.7779 (t0)
REVERT: F  348 ASP cc_start: 0.8912 (t0) cc_final: 0.8659 (t0)
REVERT: F  349 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7478 (mtp85)
REVERT: J  348 ASP cc_start: 0.8922 (t0) cc_final: 0.8555 (t0)
REVERT: J  349 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.7286 (pmt-80)
REVERT: J  372 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8306 (tm-30)
REVERT: G  324 SER cc_start: 0.8192 (m) cc_final: 0.7668 (t)
REVERT: G  349 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7425 (mmm-85)
REVERT: G  370 LYS cc_start: 0.8325 (mttt) cc_final: 0.7917 (mttp)
REVERT: I  336 GLN cc_start: 0.8314 (mp10) cc_final: 0.8045 (mp10)
REVERT: I  348 ASP cc_start: 0.8868 (t0) cc_final: 0.8627 (t70)
REVERT: I  349 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7744 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8463 (m-30) cc_final: 0.7884 (m-30)
REVERT: I  370 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8702 (ttmt)
REVERT: H  320 SER cc_start: 0.8565 (p) cc_final: 0.8348 (t)
REVERT: H  345 ASP cc_start: 0.8200 (t0) cc_final: 0.7820 (t0)
REVERT: H  349 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7035 (mmp-170)
  outliers start: 38
  outliers final: 25
  residues processed: 223
  average time/residue: 0.1099
  time to fit residues: 29.3641
Evaluate side-chains
  223 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain E residue  374 HIS
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  372 GLU
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain H residue  324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 1 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
** E 374 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 = 0.4419 r_free = 0.4419 target = 0.126939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.085616 restraints weight = 9106.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.088031 restraints weight = 4671.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.089576 restraints weight = 3088.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.090401 restraints weight = 2397.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.091062 restraints weight = 2084.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.6620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5480  Z= 0.170
  Angle     :  0.681   7.281   7320  Z= 0.352
  Chirality :  0.046   0.170    820
  Planarity :  0.004   0.029    930
  Dihedral  :  5.583  54.905    722
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 28.87 %
    Favored  : 66.29 %
  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: -2.83 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 349 
 TYR   0.010   0.001   TYR G 310 
 PHE   0.006   0.001   PHE C 346 
 HIS   0.013   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5480)
  covalent geometry    : angle       0.68111 ( 7320)
  hydrogen bonds       : bond        0.03523 (  144)
  hydrogen bonds       : angle       4.86992 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 TYR cc_start: 0.7044 (t80) cc_final: 0.6816 (t80)
REVERT: A  317 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7469 (mptt)
REVERT: A  338 GLU cc_start: 0.7633 (mp0) cc_final: 0.7379 (mp0)
REVERT: A  340 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8673 (mtpp)
REVERT: A  342 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7550 (mp0)
REVERT: A  358 ASP cc_start: 0.8851 (m-30) cc_final: 0.8645 (m-30)
REVERT: A  369 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8790 (mtmt)
REVERT: A  372 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8437 (mt-10)
REVERT: E  340 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8695 (mtpp)
REVERT: E  343 LYS cc_start: 0.9292 (mttp) cc_final: 0.8672 (pptt)
REVERT: E  348 ASP cc_start: 0.8613 (t0) cc_final: 0.7675 (p0)
REVERT: E  374 HIS cc_start: 0.5676 (OUTLIER) cc_final: 0.5361 (m170)
REVERT: E  375 LYS cc_start: 0.3667 (OUTLIER) cc_final: 0.3097 (pptt)
REVERT: B  314 ASP cc_start: 0.9087 (p0) cc_final: 0.8699 (t0)
REVERT: B  317 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7273 (mmtm)
REVERT: B  321 LYS cc_start: 0.8828 (mttm) cc_final: 0.8155 (ttmm)
REVERT: B  340 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8411 (mtpp)
REVERT: B  348 ASP cc_start: 0.8816 (t0) cc_final: 0.8589 (t0)
REVERT: B  369 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9109 (mtpt)
REVERT: D  317 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6652 (mmtm)
REVERT: D  348 ASP cc_start: 0.8832 (t0) cc_final: 0.8531 (t0)
REVERT: D  372 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8200 (mt-10)
REVERT: C  311 LYS cc_start: 0.8913 (mttt) cc_final: 0.8612 (tppt)
REVERT: C  314 ASP cc_start: 0.6412 (p0) cc_final: 0.5492 (t0)
REVERT: C  317 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7600 (mptt)
REVERT: C  369 LYS cc_start: 0.4726 (mmmt) cc_final: 0.4504 (mmtm)
REVERT: F  348 ASP cc_start: 0.8783 (t0) cc_final: 0.8508 (t0)
REVERT: F  349 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7613 (mtp-110)
REVERT: F  370 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8702 (mttt)
REVERT: J  348 ASP cc_start: 0.8848 (t0) cc_final: 0.8456 (t0)
REVERT: J  349 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7257 (pmt-80)
REVERT: J  370 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8273 (mttp)
REVERT: J  372 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8411 (tm-30)
REVERT: G  324 SER cc_start: 0.8269 (m) cc_final: 0.7875 (p)
REVERT: G  349 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7749 (mtp-110)
REVERT: G  370 LYS cc_start: 0.8274 (mttt) cc_final: 0.7912 (mttp)
REVERT: I  348 ASP cc_start: 0.8728 (t0) cc_final: 0.8508 (t70)
REVERT: I  349 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7773 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8450 (m-30) cc_final: 0.7905 (m-30)
REVERT: I  369 LYS cc_start: 0.8860 (mttt) cc_final: 0.8627 (mttt)
REVERT: H  345 ASP cc_start: 0.8185 (t0) cc_final: 0.7859 (t0)
  outliers start: 30
  outliers final: 18
  residues processed: 223
  average time/residue: 0.1077
  time to fit residues: 28.6943
Evaluate side-chains
  221 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain E residue  374 HIS
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  372 GLU
Chi-restraints excluded: chain J residue  373 THR
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain I residue  373 THR
Chi-restraints excluded: chain I residue  374 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 44 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 67 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   overall best weight:    5.0788

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

Flipped N/Q/H residues before XYZ refinement:
J 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.124591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.083900 restraints weight = 9476.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.086275 restraints weight = 4778.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.087747 restraints weight = 3135.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.088707 restraints weight = 2436.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.089279 restraints weight = 2097.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.7365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   5480  Z= 0.268
  Angle     :  0.754   6.761   7320  Z= 0.400
  Chirality :  0.047   0.147    820
  Planarity :  0.004   0.034    930
  Dihedral  :  5.600  20.178    722
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 30.00 %
    Favored  : 64.19 %
  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: -3.03 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 349 
 TYR   0.008   0.002   TYR H 310 
 PHE   0.008   0.002   PHE C 346 
 HIS   0.011   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 5480)
  covalent geometry    : angle       0.75359 ( 7320)
  hydrogen bonds       : bond        0.04588 (  144)
  hydrogen bonds       : angle       5.02194 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 226
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 TYR cc_start: 0.7388 (t80) cc_final: 0.7059 (t80)
REVERT: A  317 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7670 (mmtm)
REVERT: A  338 GLU cc_start: 0.7724 (mp0) cc_final: 0.7108 (mp0)
REVERT: A  340 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8656 (mtpp)
REVERT: A  342 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7600 (mp0)
REVERT: A  369 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8763 (mtmt)
REVERT: E  340 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8720 (mtpp)
REVERT: E  343 LYS cc_start: 0.9312 (mttp) cc_final: 0.8769 (pptt)
REVERT: E  348 ASP cc_start: 0.8627 (t0) cc_final: 0.7679 (p0)
REVERT: E  369 LYS cc_start: 0.4812 (OUTLIER) cc_final: 0.4217 (pttm)
REVERT: E  375 LYS cc_start: 0.3255 (OUTLIER) cc_final: 0.2265 (pptt)
REVERT: B  314 ASP cc_start: 0.8967 (p0) cc_final: 0.8652 (t0)
REVERT: B  317 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7354 (mmtm)
REVERT: B  321 LYS cc_start: 0.8867 (mttm) cc_final: 0.8212 (ttmm)
REVERT: B  348 ASP cc_start: 0.9008 (t0) cc_final: 0.8763 (t0)
REVERT: B  369 LYS cc_start: 0.9349 (mtpt) cc_final: 0.9073 (mtpt)
REVERT: B  375 LYS cc_start: 0.8563 (tptp) cc_final: 0.8291 (mmmt)
REVERT: D  317 LYS cc_start: 0.7395 (mmtm) cc_final: 0.6814 (mmtm)
REVERT: D  348 ASP cc_start: 0.8911 (t0) cc_final: 0.8662 (t0)
REVERT: D  372 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8228 (mt-10)
REVERT: C  311 LYS cc_start: 0.8950 (mttt) cc_final: 0.8732 (tppt)
REVERT: C  314 ASP cc_start: 0.5860 (p0) cc_final: 0.5256 (t0)
REVERT: C  317 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7629 (mptt)
REVERT: F  345 ASP cc_start: 0.8361 (t0) cc_final: 0.7938 (t0)
REVERT: F  348 ASP cc_start: 0.8925 (t0) cc_final: 0.8624 (t0)
REVERT: F  349 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7685 (mtp-110)
REVERT: F  372 GLU cc_start: 0.7205 (mp0) cc_final: 0.6875 (mp0)
REVERT: J  348 ASP cc_start: 0.9001 (t0) cc_final: 0.8557 (t0)
REVERT: J  349 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7443 (pmt-80)
REVERT: G  324 SER cc_start: 0.8400 (m) cc_final: 0.7810 (t)
REVERT: G  345 ASP cc_start: 0.8398 (t0) cc_final: 0.8194 (t0)
REVERT: G  349 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7755 (mtp-110)
REVERT: G  370 LYS cc_start: 0.8308 (mttt) cc_final: 0.7900 (ttmt)
REVERT: G  372 GLU cc_start: 0.7743 (mp0) cc_final: 0.7494 (mp0)
REVERT: I  349 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7788 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8596 (m-30) cc_final: 0.8078 (m-30)
REVERT: I  369 LYS cc_start: 0.8914 (mttt) cc_final: 0.8705 (mttt)
REVERT: H  345 ASP cc_start: 0.8255 (t0) cc_final: 0.7851 (t0)
REVERT: H  376 LEU cc_start: 0.6869 (pt) cc_final: 0.6579 (mp)
  outliers start: 36
  outliers final: 24
  residues processed: 243
  average time/residue: 0.1044
  time to fit residues: 30.5769
Evaluate side-chains
  240 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 214
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  369 LYS
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  368 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  375 LYS
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0010
   chunk 6 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:   30.0000
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    2.1792

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

Flipped N/Q/H residues before XYZ refinement:
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 374 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 = 0.4461 r_free = 0.4461 target = 0.130583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.089105 restraints weight = 9062.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.091501 restraints weight = 4781.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.093082 restraints weight = 3187.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.094116 restraints weight = 2461.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.094669 restraints weight = 2098.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.7579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5480  Z= 0.138
  Angle     :  0.666   6.359   7320  Z= 0.346
  Chirality :  0.047   0.150    820
  Planarity :  0.004   0.032    930
  Dihedral  :  4.922  17.621    720
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 31.13 %
    Favored  : 62.90 %
  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: -2.64 (0.24), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG I 349 
 TYR   0.009   0.001   TYR B 310 
 PHE   0.004   0.001   PHE H 346 
 HIS   0.012   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5480)
  covalent geometry    : angle       0.66599 ( 7320)
  hydrogen bonds       : bond        0.03575 (  144)
  hydrogen bonds       : angle       4.59080 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 212
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.7654 (mp0) cc_final: 0.7295 (mp0)
REVERT: A  340 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8672 (mtpp)
REVERT: A  342 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7535 (mp0)
REVERT: A  369 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8702 (mtmt)
REVERT: E  308 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.5034 (tp)
REVERT: E  316 SER cc_start: 0.7259 (t) cc_final: 0.7040 (p)
REVERT: E  321 LYS cc_start: 0.8739 (mttt) cc_final: 0.8135 (mmtm)
REVERT: E  340 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8657 (mtpp)
REVERT: E  343 LYS cc_start: 0.9295 (mttp) cc_final: 0.8757 (pptt)
REVERT: E  348 ASP cc_start: 0.8616 (t0) cc_final: 0.7663 (p0)
REVERT: E  369 LYS cc_start: 0.4843 (OUTLIER) cc_final: 0.4100 (pttm)
REVERT: E  375 LYS cc_start: 0.3621 (OUTLIER) cc_final: 0.2531 (pptt)
REVERT: B  314 ASP cc_start: 0.8997 (p0) cc_final: 0.8568 (t0)
REVERT: B  317 LYS cc_start: 0.7590 (ttpt) cc_final: 0.7215 (mmtm)
REVERT: B  348 ASP cc_start: 0.8865 (t0) cc_final: 0.8607 (t0)
REVERT: D  309 VAL cc_start: 0.8816 (t) cc_final: 0.8512 (m)
REVERT: D  317 LYS cc_start: 0.7336 (mmtm) cc_final: 0.6763 (mmtt)
REVERT: D  331 LYS cc_start: 0.7650 (mptt) cc_final: 0.7422 (mptt)
REVERT: D  348 ASP cc_start: 0.8808 (t0) cc_final: 0.8495 (t0)
REVERT: D  372 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8225 (mt-10)
REVERT: D  374 HIS cc_start: 0.5349 (OUTLIER) cc_final: 0.5145 (p90)
REVERT: D  376 LEU cc_start: 0.8525 (tp) cc_final: 0.8263 (mt)
REVERT: C  311 LYS cc_start: 0.8902 (mttt) cc_final: 0.8662 (tppt)
REVERT: C  314 ASP cc_start: 0.5842 (p0) cc_final: 0.5303 (t0)
REVERT: C  317 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7576 (mptt)
REVERT: C  325 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7490 (mm)
REVERT: C  343 LYS cc_start: 0.9203 (mttm) cc_final: 0.8943 (mttp)
REVERT: F  348 ASP cc_start: 0.8731 (t0) cc_final: 0.8448 (t0)
REVERT: F  349 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7700 (mtp-110)
REVERT: F  370 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8759 (mttt)
REVERT: F  372 GLU cc_start: 0.7124 (mp0) cc_final: 0.6915 (mp0)
REVERT: J  348 ASP cc_start: 0.8873 (t0) cc_final: 0.8473 (t0)
REVERT: J  349 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7078 (pmt-80)
REVERT: G  324 SER cc_start: 0.8431 (m) cc_final: 0.7853 (t)
REVERT: G  370 LYS cc_start: 0.8256 (mttt) cc_final: 0.7904 (ttmt)
REVERT: I  310 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5865 (t80)
REVERT: I  349 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7702 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8535 (m-30) cc_final: 0.8002 (m-30)
REVERT: H  336 GLN cc_start: 0.8169 (mp10) cc_final: 0.7872 (mp10)
REVERT: H  342 GLU cc_start: 0.7727 (tt0) cc_final: 0.7342 (mt-10)
REVERT: H  345 ASP cc_start: 0.8226 (t0) cc_final: 0.7882 (t0)
  outliers start: 37
  outliers final: 25
  residues processed: 230
  average time/residue: 0.1030
  time to fit residues: 28.4756
Evaluate side-chains
  233 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  369 LYS
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain D residue  374 HIS
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  372 GLU
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain I residue  374 HIS
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0870
   chunk 41 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0770
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    3.6322

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

Flipped N/Q/H residues before XYZ refinement:
** B 374 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 = 0.4424 r_free = 0.4424 target = 0.126296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.085647 restraints weight = 9416.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.088103 restraints weight = 4766.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.089674 restraints weight = 3118.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.090609 restraints weight = 2408.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.091127 restraints weight = 2075.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.7919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5480  Z= 0.199
  Angle     :  0.724   8.688   7320  Z= 0.379
  Chirality :  0.047   0.177    820
  Planarity :  0.004   0.032    930
  Dihedral  :  5.246  18.234    720
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 32.74 %
    Favored  : 61.94 %
  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: -2.73 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.18), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.006   0.001   TYR F 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.011   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 5480)
  covalent geometry    : angle       0.72441 ( 7320)
  hydrogen bonds       : bond        0.03914 (  144)
  hydrogen bonds       : angle       4.70770 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.6814 (mmtm) cc_final: 0.6486 (mmtm)
REVERT: A  338 GLU cc_start: 0.7712 (mp0) cc_final: 0.7087 (mp0)
REVERT: A  340 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8637 (mtpp)
REVERT: A  342 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7631 (mp0)
REVERT: A  369 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8739 (mtmt)
REVERT: E  316 SER cc_start: 0.7359 (t) cc_final: 0.7151 (p)
REVERT: E  340 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8676 (mtpp)
REVERT: E  343 LYS cc_start: 0.9302 (mttp) cc_final: 0.8752 (pptt)
REVERT: E  348 ASP cc_start: 0.8619 (t0) cc_final: 0.7693 (p0)
REVERT: E  369 LYS cc_start: 0.5021 (OUTLIER) cc_final: 0.4366 (pttm)
REVERT: E  375 LYS cc_start: 0.3146 (OUTLIER) cc_final: 0.2125 (pptt)
REVERT: E  376 LEU cc_start: 0.8733 (mp) cc_final: 0.8354 (mt)
REVERT: B  314 ASP cc_start: 0.9065 (p0) cc_final: 0.8470 (t0)
REVERT: B  317 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7397 (mmtm)
REVERT: B  348 ASP cc_start: 0.8907 (t0) cc_final: 0.8652 (t0)
REVERT: D  317 LYS cc_start: 0.7411 (mmtm) cc_final: 0.6852 (mmtt)
REVERT: D  331 LYS cc_start: 0.7764 (mptt) cc_final: 0.7513 (mptt)
REVERT: D  348 ASP cc_start: 0.8843 (t0) cc_final: 0.8542 (t0)
REVERT: C  311 LYS cc_start: 0.8933 (mttt) cc_final: 0.8629 (mmtm)
REVERT: C  314 ASP cc_start: 0.5793 (p0) cc_final: 0.5264 (t0)
REVERT: C  317 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7631 (mptt)
REVERT: F  348 ASP cc_start: 0.8859 (t0) cc_final: 0.8568 (t0)
REVERT: F  349 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7694 (mtp-110)
REVERT: F  370 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8780 (mttt)
REVERT: J  348 ASP cc_start: 0.8896 (t0) cc_final: 0.8523 (t0)
REVERT: J  349 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7255 (pmt-80)
REVERT: J  370 LYS cc_start: 0.8543 (mttp) cc_final: 0.8287 (mttp)
REVERT: J  375 LYS cc_start: 0.4901 (OUTLIER) cc_final: 0.4256 (pttm)
REVERT: G  324 SER cc_start: 0.8433 (m) cc_final: 0.7720 (t)
REVERT: G  345 ASP cc_start: 0.8477 (t0) cc_final: 0.8237 (t0)
REVERT: G  370 LYS cc_start: 0.8374 (mttt) cc_final: 0.7971 (ttmt)
REVERT: G  372 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: I  349 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7736 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8569 (m-30) cc_final: 0.8074 (m-30)
REVERT: H  342 GLU cc_start: 0.7900 (tt0) cc_final: 0.7469 (mt-10)
REVERT: H  345 ASP cc_start: 0.8222 (t0) cc_final: 0.7854 (t0)
REVERT: H  376 LEU cc_start: 0.6953 (pt) cc_final: 0.6586 (mp)
  outliers start: 33
  outliers final: 26
  residues processed: 230
  average time/residue: 0.0988
  time to fit residues: 27.5720
Evaluate side-chains
  243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  369 LYS
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  373 THR
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain J residue  375 LYS
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 35 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 374 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 = 0.4401 r_free = 0.4401 target = 0.124232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.084813 restraints weight = 9467.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.087185 restraints weight = 4780.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.088723 restraints weight = 3149.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.089592 restraints weight = 2434.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.090185 restraints weight = 2104.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.8342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   5480  Z= 0.294
  Angle     :  0.818   9.630   7320  Z= 0.429
  Chirality :  0.048   0.145    820
  Planarity :  0.004   0.037    930
  Dihedral  :  5.861  21.132    720
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 31.94 %
    Favored  : 61.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.11 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG J 349 
 TYR   0.003   0.001   TYR J 310 
 PHE   0.006   0.001   PHE H 346 
 HIS   0.012   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 5480)
  covalent geometry    : angle       0.81828 ( 7320)
  hydrogen bonds       : bond        0.04476 (  144)
  hydrogen bonds       : angle       4.96252 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.7869 (mp0) cc_final: 0.7268 (mp0)
REVERT: A  340 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8683 (mtpp)
REVERT: A  342 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7636 (mp0)
REVERT: A  369 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8814 (mtmt)
REVERT: E  340 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8725 (mtpp)
REVERT: E  343 LYS cc_start: 0.9280 (mttp) cc_final: 0.8799 (pptt)
REVERT: E  348 ASP cc_start: 0.8621 (t0) cc_final: 0.7619 (p0)
REVERT: E  375 LYS cc_start: 0.3520 (OUTLIER) cc_final: 0.1696 (pptt)
REVERT: B  314 ASP cc_start: 0.8911 (p0) cc_final: 0.8385 (t0)
REVERT: B  317 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7511 (mmtm)
REVERT: B  348 ASP cc_start: 0.8970 (t0) cc_final: 0.8756 (t0)
REVERT: D  331 LYS cc_start: 0.7796 (mptt) cc_final: 0.7563 (mptt)
REVERT: D  348 ASP cc_start: 0.8906 (t0) cc_final: 0.8668 (t0)
REVERT: D  374 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.4427 (p-80)
REVERT: D  375 LYS cc_start: 0.8117 (tptp) cc_final: 0.7906 (ptmm)
REVERT: C  311 LYS cc_start: 0.8951 (mttt) cc_final: 0.8678 (mmtm)
REVERT: C  317 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7553 (mptt)
REVERT: C  342 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: F  348 ASP cc_start: 0.8938 (t0) cc_final: 0.8679 (t0)
REVERT: F  349 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7745 (mtp-110)
REVERT: F  370 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8801 (ttmt)
REVERT: J  348 ASP cc_start: 0.8984 (t0) cc_final: 0.8622 (t0)
REVERT: J  349 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7317 (pmt-80)
REVERT: G  342 GLU cc_start: 0.8229 (tt0) cc_final: 0.7965 (mt-10)
REVERT: G  345 ASP cc_start: 0.8490 (t0) cc_final: 0.8288 (t0)
REVERT: G  370 LYS cc_start: 0.8478 (mttt) cc_final: 0.8097 (ttmt)
REVERT: I  311 LYS cc_start: 0.8814 (mttt) cc_final: 0.8393 (mttp)
REVERT: I  349 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7810 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8639 (m-30) cc_final: 0.8139 (m-30)
REVERT: H  342 GLU cc_start: 0.7914 (tt0) cc_final: 0.7474 (mt-10)
REVERT: H  345 ASP cc_start: 0.8277 (t0) cc_final: 0.7911 (t0)
  outliers start: 41
  outliers final: 33
  residues processed: 238
  average time/residue: 0.0957
  time to fit residues: 27.8827
Evaluate side-chains
  252 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain D residue  374 HIS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  368 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain I residue  308 ILE
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN
** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.177346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.132642 restraints weight = 11293.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.135021 restraints weight = 4602.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.136505 restraints weight = 2850.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.137023 restraints weight = 2261.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.137023 restraints weight = 2093.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.8482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5480  Z= 0.176
  Angle     :  0.767  10.337   7320  Z= 0.394
  Chirality :  0.047   0.158    820
  Planarity :  0.004   0.037    930
  Dihedral  :  5.308  17.771    720
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 34.03 %
    Favored  : 60.16 %
  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: -2.86 (0.23), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.17), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.006   0.001   TYR B 310 
 PHE   0.004   0.001   PHE H 346 
 HIS   0.012   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 5480)
  covalent geometry    : angle       0.76671 ( 7320)
  hydrogen bonds       : bond        0.03609 (  144)
  hydrogen bonds       : angle       4.59748 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 222
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.7896 (mp0) cc_final: 0.7326 (mp0)
REVERT: A  340 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8704 (mtpp)
REVERT: A  342 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7606 (mp0)
REVERT: A  369 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8770 (mtmt)
REVERT: E  340 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8636 (mtpp)
REVERT: E  343 LYS cc_start: 0.9250 (mttp) cc_final: 0.8867 (pptt)
REVERT: E  348 ASP cc_start: 0.8480 (t0) cc_final: 0.7688 (p0)
REVERT: E  375 LYS cc_start: 0.3728 (OUTLIER) cc_final: 0.2191 (pptt)
REVERT: B  307 GLN cc_start: 0.4112 (OUTLIER) cc_final: 0.3077 (pm20)
REVERT: B  311 LYS cc_start: 0.9227 (mttt) cc_final: 0.8965 (mmtt)
REVERT: B  314 ASP cc_start: 0.8721 (p0) cc_final: 0.8215 (t0)
REVERT: B  317 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7473 (mmtm)
REVERT: D  317 LYS cc_start: 0.7673 (mmtp) cc_final: 0.7260 (mmtm)
REVERT: D  348 ASP cc_start: 0.8728 (t0) cc_final: 0.8476 (t0)
REVERT: D  374 HIS cc_start: 0.4968 (OUTLIER) cc_final: 0.4658 (p-80)
REVERT: D  376 LEU cc_start: 0.8109 (mp) cc_final: 0.7848 (mp)
REVERT: D  377 THR cc_start: 0.6746 (m) cc_final: 0.6278 (m)
REVERT: C  317 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7732 (mptt)
REVERT: C  325 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7582 (mm)
REVERT: C  343 LYS cc_start: 0.9243 (mttm) cc_final: 0.9007 (mttp)
REVERT: F  348 ASP cc_start: 0.8721 (t0) cc_final: 0.8517 (t0)
REVERT: F  349 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7960 (mtp-110)
REVERT: F  370 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8729 (mttt)
REVERT: F  376 LEU cc_start: 0.8313 (mt) cc_final: 0.7998 (mt)
REVERT: J  348 ASP cc_start: 0.8803 (t0) cc_final: 0.8485 (t0)
REVERT: J  349 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7364 (pmt-80)
REVERT: G  370 LYS cc_start: 0.8346 (mttt) cc_final: 0.7954 (ttmt)
REVERT: I  311 LYS cc_start: 0.8772 (mttt) cc_final: 0.8361 (mttp)
REVERT: I  349 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7918 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8623 (m-30) cc_final: 0.8157 (m-30)
REVERT: H  342 GLU cc_start: 0.7867 (tt0) cc_final: 0.7552 (mt-10)
  outliers start: 36
  outliers final: 27
  residues processed: 236
  average time/residue: 0.0971
  time to fit residues: 28.0322
Evaluate side-chains
  247 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 216
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  307 GLN
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain D residue  374 HIS
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain G residue  374 HIS
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 307 GLN
J 307 GLN
G 307 GLN
** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.122490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.083047 restraints weight = 9740.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.085326 restraints weight = 5057.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.086817 restraints weight = 3370.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.087746 restraints weight = 2624.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.088165 restraints weight = 2261.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.8753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   5480  Z= 0.303
  Angle     :  0.909  10.971   7320  Z= 0.477
  Chirality :  0.049   0.152    820
  Planarity :  0.004   0.038    930
  Dihedral  :  6.002  20.809    720
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 32.90 %
    Favored  : 60.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.16), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.005   0.001   TYR B 310 
 PHE   0.006   0.001   PHE H 346 
 HIS   0.012   0.002   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 5480)
  covalent geometry    : angle       0.90918 ( 7320)
  hydrogen bonds       : bond        0.04590 (  144)
  hydrogen bonds       : angle       4.89015 (  432)

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 219
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.7677 (mp0) cc_final: 0.7007 (mp0)
REVERT: A  340 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8626 (mtpp)
REVERT: A  342 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7605 (mp0)
REVERT: A  369 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8848 (mtmt)
REVERT: A  372 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8639 (mt-10)
REVERT: E  340 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8733 (mtpp)
REVERT: E  343 LYS cc_start: 0.9331 (mttp) cc_final: 0.8776 (pptt)
REVERT: E  348 ASP cc_start: 0.8661 (t0) cc_final: 0.7596 (p0)
REVERT: E  375 LYS cc_start: 0.3574 (OUTLIER) cc_final: 0.2494 (pptt)
REVERT: B  311 LYS cc_start: 0.9232 (mttt) cc_final: 0.9019 (mmtt)
REVERT: B  314 ASP cc_start: 0.8918 (p0) cc_final: 0.8434 (t0)
REVERT: B  317 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7402 (mmtm)
REVERT: D  317 LYS cc_start: 0.7557 (mmtp) cc_final: 0.7056 (mmtm)
REVERT: D  348 ASP cc_start: 0.8904 (t0) cc_final: 0.8627 (t0)
REVERT: C  307 GLN cc_start: 0.3209 (mm-40) cc_final: 0.2939 (mm-40)
REVERT: C  317 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7558 (mptt)
REVERT: F  348 ASP cc_start: 0.8897 (t0) cc_final: 0.8602 (t0)
REVERT: F  349 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7561 (mtp-110)
REVERT: F  370 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8692 (mttt)
REVERT: J  348 ASP cc_start: 0.8984 (t0) cc_final: 0.8613 (t0)
REVERT: J  349 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.7060 (pmt-80)
REVERT: G  370 LYS cc_start: 0.8438 (mttt) cc_final: 0.8031 (ttmt)
REVERT: I  311 LYS cc_start: 0.8762 (mttt) cc_final: 0.8379 (mttp)
REVERT: I  349 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7638 (mtp-110)
REVERT: I  358 ASP cc_start: 0.8539 (m-30) cc_final: 0.8028 (m-30)
REVERT: H  342 GLU cc_start: 0.7878 (tt0) cc_final: 0.7386 (mt-10)
  outliers start: 38
  outliers final: 30
  residues processed: 233
  average time/residue: 0.0910
  time to fit residues: 26.0862
Evaluate side-chains
  243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 212
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  374 HIS
Chi-restraints excluded: chain E residue  313 VAL
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain E residue  375 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain D residue  310 TYR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  368 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  324 SER
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  316 SER
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain H residue  316 SER
Chi-restraints excluded: chain H residue  373 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 21 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 307 GLN
G 307 GLN
** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.198530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.141634 restraints weight = 11986.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.144173 restraints weight = 4832.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.145719 restraints weight = 2915.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.146395 restraints weight = 2282.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.146628 restraints weight = 2079.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.8909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5480  Z= 0.265
  Angle     :  0.894  10.613   7320  Z= 0.467
  Chirality :  0.049   0.157    820
  Planarity :  0.004   0.038    930
  Dihedral  :  5.896  19.541    720
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 33.71 %
    Favored  : 60.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.27 (0.22), residues: 690
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.16), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.004   0.001   TYR B 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.013   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 5480)
  covalent geometry    : angle       0.89353 ( 7320)
  hydrogen bonds       : bond        0.04718 (  144)
  hydrogen bonds       : angle       4.88390 (  432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1243.15 seconds
wall clock time: 22 minutes 13.25 seconds (1333.25 seconds total)