Starting phenix.real_space_refine
on Tue Mar  3 11:08:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tzx_56478/03_2026/9tzx_56478.cif"
  }
  resolution = 2.75
  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=   0.002
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      10      5.16       5
     C    1685      2.51       5
     N     495      2.21       5
     O     510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  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: 2700
  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
  Time building chain proxies: 0.47, per 1000 atoms: 0.17
  Number of scatterers: 2700
  At special positions: 0
  Unit cell: (74.52, 89.64, 50.76, 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      10     16.00
     O     510      8.00
     N     495      7.00
     C    1685      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: 0.14
  Conformation dependent library (CDL) restraints added in 63.5 milliseconds
  

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  620

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 33.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 308 through 310
      removed outlier: 6.400A  pdb=" N   ILE E 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE A 308 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE B 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 315
      removed outlier: 6.245A  pdb=" N   ASP E 314 " --> pdb=" O   LEU D 315 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP A 314 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASP B 314 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 318 through 319
      removed outlier: 6.250A  pdb=" N   VAL E 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL B 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 328 through 330
      removed outlier: 6.392A  pdb=" N   ILE E 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ILE B 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 336 through 345
      removed outlier: 6.466A  pdb=" N   MET E 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   LYS D 340 " --> pdb=" O   MET E 337 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   VAL E 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   GLU D 342 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   SER E 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU D 344 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LYS E 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU A 344 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ASP D 345 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   MET A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   LYS B 340 " --> pdb=" O   MET A 337 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   GLU B 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   SER A 341 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   LEU B 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LYS A 343 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   MET B 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   LYS C 340 " --> pdb=" O   MET B 337 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   VAL B 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   GLU C 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   SER B 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LEU C 344 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   LYS B 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 350 through 351
      removed outlier: 6.631A  pdb=" N   VAL E 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 357
      removed outlier: 6.025A  pdb=" N   ILE E 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU D 357 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   SER E 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   ILE B 354 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LEU C 357 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   SER B 356 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 360 through 362
      removed outlier: 6.492A  pdb=" N   THR E 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR B 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 374 through 376
      removed outlier: 6.536A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)

    26 hydrogen bonds defined for protein.
    78 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: 0.29

  Time building geometry restraints manager: 0.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 890
        1.34 -     1.46: 357
        1.46 -     1.57: 1478
        1.57 -     1.69: 0
        1.69 -     1.80: 15
  Bond restraints: 2740
  Sorted by residual:
  bond pdb=" C   GLY E 355 "
       pdb=" O   GLY E 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.229  0.008 7.00e-03 2.04e+04 1.39e+00
  bond pdb=" C   GLY A 355 "
       pdb=" O   GLY A 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.229  0.008 7.00e-03 2.04e+04 1.39e+00
  bond pdb=" C   GLY D 355 "
       pdb=" O   GLY D 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.229  0.008 7.00e-03 2.04e+04 1.35e+00
  bond pdb=" C   GLY B 355 "
       pdb=" O   GLY B 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.229  0.008 7.00e-03 2.04e+04 1.25e+00
  bond pdb=" C   GLY C 355 "
       pdb=" O   GLY C 355 "
    ideal  model  delta    sigma   weight residual
    1.237  1.229  0.008 7.00e-03 2.04e+04 1.25e+00
  ... (remaining 2735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 3369
        1.30 -     2.60: 221
        2.60 -     3.90: 45
        3.90 -     5.19: 10
        5.19 -     6.49: 15
  Bond angle restraints: 3660
  Sorted by residual:
  angle pdb=" CA  LYS D 311 "
        pdb=" C   LYS D 311 "
        pdb=" N   PRO D 312 "
      ideal   model   delta    sigma   weight residual
     117.59  120.26   -2.67 1.03e+00 9.43e-01 6.71e+00
  angle pdb=" CA  LYS A 311 "
        pdb=" C   LYS A 311 "
        pdb=" N   PRO A 312 "
      ideal   model   delta    sigma   weight residual
     117.59  120.25   -2.66 1.03e+00 9.43e-01 6.66e+00
  angle pdb=" CA  LYS C 311 "
        pdb=" C   LYS C 311 "
        pdb=" N   PRO C 312 "
      ideal   model   delta    sigma   weight residual
     117.59  120.24   -2.65 1.03e+00 9.43e-01 6.64e+00
  angle pdb=" CA  LYS B 311 "
        pdb=" C   LYS B 311 "
        pdb=" N   PRO B 312 "
      ideal   model   delta    sigma   weight residual
     117.59  120.21   -2.62 1.03e+00 9.43e-01 6.49e+00
  angle pdb=" CA  LYS E 311 "
        pdb=" C   LYS E 311 "
        pdb=" N   PRO E 312 "
      ideal   model   delta    sigma   weight residual
     117.59  120.20   -2.61 1.03e+00 9.43e-01 6.42e+00
  ... (remaining 3655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.95: 1360
       10.95 -    21.89: 155
       21.89 -    32.84: 91
       32.84 -    43.79: 59
       43.79 -    54.74: 20
  Dihedral angle restraints: 1685
    sinusoidal: 710
      harmonic: 975
  Sorted by residual:
  dihedral pdb=" CB  LYS D 369 "
           pdb=" CG  LYS D 369 "
           pdb=" CD  LYS D 369 "
           pdb=" CE  LYS D 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -125.26  -54.74     3      1.50e+01 4.44e-03 9.30e+00
  dihedral pdb=" CB  LYS C 369 "
           pdb=" CG  LYS C 369 "
           pdb=" CD  LYS C 369 "
           pdb=" CE  LYS C 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.27  -54.73     3      1.50e+01 4.44e-03 9.30e+00
  dihedral pdb=" CB  LYS B 369 "
           pdb=" CG  LYS B 369 "
           pdb=" CD  LYS B 369 "
           pdb=" CE  LYS B 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.27  -54.73     3      1.50e+01 4.44e-03 9.30e+00
  ... (remaining 1682 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 190
       0.026 -    0.052: 122
       0.052 -    0.078: 33
       0.078 -    0.104: 34
       0.104 -    0.130: 31
  Chirality restraints: 410
  Sorted by residual:
  chirality pdb=" CA  VAL A 350 "
            pdb=" N   VAL A 350 "
            pdb=" C   VAL A 350 "
            pdb=" CB  VAL A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL B 350 "
            pdb=" N   VAL B 350 "
            pdb=" C   VAL B 350 "
            pdb=" CB  VAL B 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL D 350 "
            pdb=" N   VAL D 350 "
            pdb=" C   VAL D 350 "
            pdb=" CB  VAL D 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 407 not shown)

  Planarity restraints: 465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "   -0.011 5.00e-02 4.00e+02   1.64e-02 4.30e-01
        pdb=" N   PRO B 364 "    0.028 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "   -0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "   -0.009 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 363 "   -0.011 5.00e-02 4.00e+02   1.64e-02 4.28e-01
        pdb=" N   PRO A 364 "    0.028 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "   -0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO A 364 "   -0.009 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 363 "   -0.011 5.00e-02 4.00e+02   1.63e-02 4.24e-01
        pdb=" N   PRO C 364 "    0.028 5.00e-02 4.00e+02
        pdb=" CA  PRO C 364 "   -0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO C 364 "   -0.009 5.00e-02 4.00e+02
  ... (remaining 462 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 1572
        3.09 -     3.54: 2429
        3.54 -     3.99: 3766
        3.99 -     4.45: 4140
        4.45 -     4.90: 7237
  Nonbonded interactions: 19144
  Sorted by model distance:
  nonbonded pdb=" N   ASP C 348 "
            pdb=" O   ASP C 348 "
     model   vdw
     2.635 2.496
  nonbonded pdb=" N   ASP A 348 "
            pdb=" O   ASP A 348 "
     model   vdw
     2.636 2.496
  nonbonded pdb=" N   ASP B 348 "
            pdb=" O   ASP B 348 "
     model   vdw
     2.636 2.496
  nonbonded pdb=" N   ASP D 348 "
            pdb=" O   ASP D 348 "
     model   vdw
     2.636 2.496
  nonbonded pdb=" N   ASP E 348 "
            pdb=" O   ASP E 348 "
     model   vdw
     2.636 2.496
  ... (remaining 19139 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
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      :  0.005   0.033   2740  Z= 0.246
  Angle     :  0.846   6.493   3660  Z= 0.467
  Chirality :  0.050   0.130    410
  Planarity :  0.003   0.016    465
  Dihedral  : 15.430  54.736   1065
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 26.13 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.97 (0.33), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.25), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C 349 
 TYR   0.004   0.002   TYR D 310 
 PHE   0.003   0.001   PHE C 346 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 2740)
  covalent geometry    : angle       0.84552 ( 3660)
  hydrogen bonds       : bond        0.24548 (   26)
  hydrogen bonds       : angle       7.93346 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8228 (mt0) cc_final: 0.7569 (tt0)
REVERT: A  337 MET cc_start: 0.7634 (mpt) cc_final: 0.7425 (mpt)
REVERT: A  356 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8065 (t)
REVERT: A  372 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7671 (mt-10)
REVERT: A  375 LYS cc_start: 0.8409 (tttt) cc_final: 0.8069 (ttmm)
REVERT: E  336 GLN cc_start: 0.8583 (mt0) cc_final: 0.8331 (tt0)
REVERT: E  372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: E  375 LYS cc_start: 0.8651 (tttt) cc_final: 0.8340 (ttmm)
REVERT: D  325 LEU cc_start: 0.7748 (tp) cc_final: 0.7467 (tp)
REVERT: D  336 GLN cc_start: 0.8224 (mt0) cc_final: 0.7627 (tt0)
REVERT: D  337 MET cc_start: 0.7881 (mpt) cc_final: 0.7462 (mpt)
REVERT: C  336 GLN cc_start: 0.8240 (mt0) cc_final: 0.7827 (tt0)
REVERT: C  337 MET cc_start: 0.8188 (mpt) cc_final: 0.7933 (mpt)
REVERT: C  372 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: C  375 LYS cc_start: 0.8471 (tttt) cc_final: 0.8200 (tttm)
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.4143
  time to fit residues: 21.3443
Evaluate side-chains
  49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain C residue  356 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
B 359 ASN
D 359 ASN
C 359 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.102706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.078135 restraints weight = 3661.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 3.12
r_work: 0.3347 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2740  Z= 0.171
  Angle     :  0.608   6.435   3660  Z= 0.308
  Chirality :  0.049   0.132    410
  Planarity :  0.003   0.016    465
  Dihedral  :  5.171  14.731    363
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 23.55 %
    Favored  : 73.87 %
  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: -2.80 (0.35), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.26), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.020   0.005   TYR D 310 
 PHE   0.002   0.001   PHE B 346 
 HIS   0.005   0.002   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 2740)
  covalent geometry    : angle       0.60806 ( 3660)
  hydrogen bonds       : bond        0.02891 (   26)
  hydrogen bonds       : angle       4.79801 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7613 (mpt) cc_final: 0.7412 (mpt)
REVERT: A  356 SER cc_start: 0.8520 (m) cc_final: 0.8225 (t)
REVERT: A  372 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7526 (mt-10)
REVERT: A  375 LYS cc_start: 0.8351 (tttt) cc_final: 0.8110 (ttpt)
REVERT: E  314 ASP cc_start: 0.8361 (t0) cc_final: 0.8153 (t0)
REVERT: E  372 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7759 (mt-10)
REVERT: E  375 LYS cc_start: 0.8504 (tttt) cc_final: 0.8303 (ttmm)
REVERT: B  331 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8066 (mttt)
REVERT: B  338 GLU cc_start: 0.8205 (tt0) cc_final: 0.7646 (tm-30)
REVERT: D  325 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7570 (tp)
REVERT: D  336 GLN cc_start: 0.8167 (mt0) cc_final: 0.7634 (tt0)
REVERT: D  337 MET cc_start: 0.7419 (mpt) cc_final: 0.7023 (mpt)
REVERT: D  338 GLU cc_start: 0.7827 (tt0) cc_final: 0.7454 (tm-30)
REVERT: C  372 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: C  375 LYS cc_start: 0.8098 (tttt) cc_final: 0.7773 (ttmm)
  outliers start: 8
  outliers final: 3
  residues processed: 47
  average time/residue: 0.4976
  time to fit residues: 23.9722
Evaluate side-chains
  46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.102653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.078445 restraints weight = 3740.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 3.05
r_work: 0.3353 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2740  Z= 0.165
  Angle     :  0.577   4.333   3660  Z= 0.295
  Chirality :  0.048   0.124    410
  Planarity :  0.002   0.016    465
  Dihedral  :  5.107  15.228    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 22.26 %
    Favored  : 75.81 %
  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: -2.63 (0.36), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.27), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.016   0.004   TYR E 310 
 PHE   0.002   0.001   PHE D 346 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 2740)
  covalent geometry    : angle       0.57696 ( 3660)
  hydrogen bonds       : bond        0.02835 (   26)
  hydrogen bonds       : angle       4.52461 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7945 (mpt) cc_final: 0.7638 (mpt)
REVERT: A  372 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7722 (mt-10)
REVERT: A  375 LYS cc_start: 0.8502 (tttt) cc_final: 0.8257 (ttmm)
REVERT: E  314 ASP cc_start: 0.8496 (t0) cc_final: 0.8288 (t0)
REVERT: E  325 LEU cc_start: 0.7955 (tp) cc_final: 0.7740 (tp)
REVERT: E  372 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: B  331 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8189 (mttt)
REVERT: B  338 GLU cc_start: 0.8321 (tt0) cc_final: 0.8010 (mp0)
REVERT: D  325 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7603 (tp)
REVERT: D  336 GLN cc_start: 0.8253 (mt0) cc_final: 0.7798 (tt0)
REVERT: D  337 MET cc_start: 0.7811 (mpt) cc_final: 0.7411 (mpt)
REVERT: D  338 GLU cc_start: 0.7979 (tt0) cc_final: 0.7665 (tm-30)
REVERT: C  372 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8191 (mt-10)
  outliers start: 6
  outliers final: 4
  residues processed: 43
  average time/residue: 0.4966
  time to fit residues: 21.9771
Evaluate side-chains
  45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0000
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.104522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.080371 restraints weight = 3591.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 3.01
r_work: 0.3393 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2740  Z= 0.110
  Angle     :  0.519   3.914   3660  Z= 0.263
  Chirality :  0.047   0.121    410
  Planarity :  0.002   0.013    465
  Dihedral  :  4.833  14.195    360
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 24.19 %
    Favored  : 74.19 %
  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: -2.43 (0.37), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.011   0.003   TYR E 310 
 PHE   0.001   0.000   PHE A 346 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2740)
  covalent geometry    : angle       0.51874 ( 3660)
  hydrogen bonds       : bond        0.01875 (   26)
  hydrogen bonds       : angle       4.32542 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7987 (mpt) cc_final: 0.7664 (mpt)
REVERT: A  372 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7714 (mt-10)
REVERT: A  375 LYS cc_start: 0.8505 (tttt) cc_final: 0.8264 (ttmm)
REVERT: E  314 ASP cc_start: 0.8529 (t0) cc_final: 0.8295 (t0)
REVERT: E  325 LEU cc_start: 0.7709 (tp) cc_final: 0.7446 (tp)
REVERT: E  372 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  338 GLU cc_start: 0.8307 (tt0) cc_final: 0.7999 (mp0)
REVERT: D  325 LEU cc_start: 0.8011 (tp) cc_final: 0.7638 (tp)
REVERT: D  336 GLN cc_start: 0.8312 (mt0) cc_final: 0.7772 (tt0)
REVERT: D  337 MET cc_start: 0.7749 (mpt) cc_final: 0.7387 (mpt)
REVERT: D  338 GLU cc_start: 0.7978 (tt0) cc_final: 0.7670 (tm-30)
REVERT: C  372 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8158 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 41
  average time/residue: 0.4974
  time to fit residues: 21.0000
Evaluate side-chains
  41 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.101659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.077351 restraints weight = 3731.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 3.05
r_work: 0.3320 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2740  Z= 0.220
  Angle     :  0.603   4.198   3660  Z= 0.316
  Chirality :  0.049   0.124    410
  Planarity :  0.003   0.017    465
  Dihedral  :  5.212  15.852    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 24.84 %
    Favored  : 73.23 %
  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: -2.44 (0.37), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.019   0.005   TYR A 310 
 PHE   0.003   0.001   PHE B 346 
 HIS   0.004   0.002   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 2740)
  covalent geometry    : angle       0.60282 ( 3660)
  hydrogen bonds       : bond        0.03049 (   26)
  hydrogen bonds       : angle       4.46102 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7969 (mpt) cc_final: 0.7651 (mpt)
REVERT: A  372 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7757 (mt-10)
REVERT: A  375 LYS cc_start: 0.8623 (tttt) cc_final: 0.8359 (ttmm)
REVERT: E  314 ASP cc_start: 0.8501 (t0) cc_final: 0.8282 (t0)
REVERT: E  325 LEU cc_start: 0.7864 (tp) cc_final: 0.7637 (tp)
REVERT: E  372 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7896 (mt-10)
REVERT: B  338 GLU cc_start: 0.8317 (tt0) cc_final: 0.7978 (mp0)
REVERT: D  325 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7659 (tp)
REVERT: D  337 MET cc_start: 0.7785 (mpt) cc_final: 0.7523 (mpt)
REVERT: D  338 GLU cc_start: 0.7988 (tt0) cc_final: 0.7747 (mp0)
REVERT: C  372 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8144 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 41
  average time/residue: 0.4595
  time to fit residues: 19.3881
Evaluate side-chains
  42 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.102977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.078809 restraints weight = 3731.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 3.04
r_work: 0.3361 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2740  Z= 0.150
  Angle     :  0.547   4.485   3660  Z= 0.283
  Chirality :  0.047   0.121    410
  Planarity :  0.002   0.016    465
  Dihedral  :  5.065  15.457    360
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.52 %
    Favored  : 73.23 %
  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: -2.36 (0.38), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.014   0.003   TYR E 310 
 PHE   0.001   0.000   PHE B 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2740)
  covalent geometry    : angle       0.54690 ( 3660)
  hydrogen bonds       : bond        0.02291 (   26)
  hydrogen bonds       : angle       4.34832 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  337 MET cc_start: 0.8000 (mpt) cc_final: 0.7693 (mpt)
REVERT: A  372 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7747 (mt-10)
REVERT: A  375 LYS cc_start: 0.8520 (tttt) cc_final: 0.8283 (ttmm)
REVERT: E  314 ASP cc_start: 0.8456 (t0) cc_final: 0.8237 (t0)
REVERT: E  325 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7531 (tp)
REVERT: E  348 ASP cc_start: 0.8032 (t0) cc_final: 0.7578 (t0)
REVERT: E  349 ARG cc_start: 0.7839 (ttm170) cc_final: 0.6356 (pmt-80)
REVERT: E  372 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7888 (mt-10)
REVERT: B  338 GLU cc_start: 0.8304 (tt0) cc_final: 0.8006 (mp0)
REVERT: D  325 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7706 (tp)
REVERT: D  337 MET cc_start: 0.7776 (mpt) cc_final: 0.7521 (mpt)
REVERT: D  338 GLU cc_start: 0.7954 (tt0) cc_final: 0.7739 (mp0)
REVERT: D  345 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8041 (m-30)
REVERT: C  372 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8171 (mt-10)
  outliers start: 7
  outliers final: 3
  residues processed: 43
  average time/residue: 0.5433
  time to fit residues: 24.0070
Evaluate side-chains
  44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.104041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.079850 restraints weight = 3645.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 3.02
r_work: 0.3380 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2740  Z= 0.126
  Angle     :  0.524   4.058   3660  Z= 0.270
  Chirality :  0.047   0.121    410
  Planarity :  0.002   0.015    465
  Dihedral  :  4.895  14.891    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.52 %
    Favored  : 73.23 %
  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: -2.29 (0.38), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.012   0.003   TYR E 310 
 PHE   0.001   0.000   PHE A 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2740)
  covalent geometry    : angle       0.52363 ( 3660)
  hydrogen bonds       : bond        0.02004 (   26)
  hydrogen bonds       : angle       4.26974 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7978 (mpt) cc_final: 0.7682 (mpt)
REVERT: A  375 LYS cc_start: 0.8499 (tttt) cc_final: 0.8266 (ttmm)
REVERT: E  314 ASP cc_start: 0.8455 (t0) cc_final: 0.8232 (t0)
REVERT: E  325 LEU cc_start: 0.7631 (tp) cc_final: 0.7369 (tp)
REVERT: E  349 ARG cc_start: 0.7824 (ttm170) cc_final: 0.6364 (pmt-80)
REVERT: E  372 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: B  338 GLU cc_start: 0.8297 (tt0) cc_final: 0.8011 (mp0)
REVERT: D  325 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7674 (tp)
REVERT: D  337 MET cc_start: 0.7808 (mpt) cc_final: 0.7572 (mpt)
REVERT: D  345 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8023 (m-30)
REVERT: C  372 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8168 (mt-10)
  outliers start: 7
  outliers final: 3
  residues processed: 43
  average time/residue: 0.5467
  time to fit residues: 24.1381
Evaluate side-chains
  42 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.100761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.076203 restraints weight = 3862.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 3.11
r_work: 0.3314 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2740  Z= 0.248
  Angle     :  0.627   4.835   3660  Z= 0.331
  Chirality :  0.049   0.124    410
  Planarity :  0.003   0.017    465
  Dihedral  :  5.307  16.648    360
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.84 %
    Favored  : 72.90 %
  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: -2.44 (0.37), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.020   0.005   TYR D 310 
 PHE   0.003   0.001   PHE B 346 
 HIS   0.005   0.002   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 2740)
  covalent geometry    : angle       0.62657 ( 3660)
  hydrogen bonds       : bond        0.03273 (   26)
  hydrogen bonds       : angle       4.53932 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  337 MET cc_start: 0.7991 (mpt) cc_final: 0.7673 (mpt)
REVERT: A  375 LYS cc_start: 0.8611 (tttt) cc_final: 0.8370 (ttmm)
REVERT: E  314 ASP cc_start: 0.8474 (t0) cc_final: 0.8244 (t0)
REVERT: E  325 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7591 (tp)
REVERT: E  348 ASP cc_start: 0.8080 (t0) cc_final: 0.7706 (t0)
REVERT: E  349 ARG cc_start: 0.7848 (ttm170) cc_final: 0.6366 (pmt-80)
REVERT: E  372 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7901 (mt-10)
REVERT: B  338 GLU cc_start: 0.8342 (tt0) cc_final: 0.7912 (mp0)
REVERT: D  325 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7698 (tp)
REVERT: D  345 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8070 (m-30)
REVERT: C  372 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8192 (mt-10)
  outliers start: 7
  outliers final: 3
  residues processed: 42
  average time/residue: 0.4797
  time to fit residues: 20.7546
Evaluate side-chains
  44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    3.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.100871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.076358 restraints weight = 3832.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 3.09
r_work: 0.3318 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2740  Z= 0.246
  Angle     :  0.636   5.223   3660  Z= 0.335
  Chirality :  0.049   0.124    410
  Planarity :  0.003   0.015    465
  Dihedral  :  5.333  16.806    360
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.19 %
    Favored  : 73.55 %
  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: -2.43 (0.37), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.019   0.005   TYR D 310 
 PHE   0.003   0.001   PHE B 346 
 HIS   0.005   0.002   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 2740)
  covalent geometry    : angle       0.63596 ( 3660)
  hydrogen bonds       : bond        0.03248 (   26)
  hydrogen bonds       : angle       4.56829 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8417 (t0) cc_final: 0.8121 (t0)
REVERT: A  375 LYS cc_start: 0.8619 (tttt) cc_final: 0.8373 (ttmm)
REVERT: E  314 ASP cc_start: 0.8458 (t0) cc_final: 0.8220 (t0)
REVERT: E  325 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7576 (tp)
REVERT: E  348 ASP cc_start: 0.8113 (t0) cc_final: 0.7700 (t0)
REVERT: E  349 ARG cc_start: 0.7879 (ttm170) cc_final: 0.6373 (pmt-80)
REVERT: E  372 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7925 (mt-10)
REVERT: B  338 GLU cc_start: 0.8351 (tt0) cc_final: 0.7936 (mp0)
REVERT: D  325 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7641 (tp)
REVERT: C  372 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8193 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 42
  average time/residue: 0.4848
  time to fit residues: 20.8961
Evaluate side-chains
  43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 31 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.6988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.102899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.078590 restraints weight = 3764.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 3.06
r_work: 0.3369 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2740  Z= 0.136
  Angle     :  0.575   6.173   3660  Z= 0.297
  Chirality :  0.048   0.122    410
  Planarity :  0.002   0.015    465
  Dihedral  :  5.023  15.286    360
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 25.48 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.31 (0.38), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG D 349 
 TYR   0.012   0.003   TYR E 310 
 PHE   0.001   0.000   PHE B 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2740)
  covalent geometry    : angle       0.57526 ( 3660)
  hydrogen bonds       : bond        0.02095 (   26)
  hydrogen bonds       : angle       4.35521 (   78)

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

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

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  690 Ramachandran restraints generated.
    345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8384 (t0) cc_final: 0.8107 (t0)
REVERT: A  375 LYS cc_start: 0.8518 (tttt) cc_final: 0.8281 (ttmm)
REVERT: E  314 ASP cc_start: 0.8442 (t0) cc_final: 0.8228 (t0)
REVERT: E  325 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7394 (tp)
REVERT: E  348 ASP cc_start: 0.8135 (t0) cc_final: 0.7773 (t0)
REVERT: E  349 ARG cc_start: 0.7865 (ttm170) cc_final: 0.6370 (pmt-80)
REVERT: E  372 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7854 (mt-10)
REVERT: B  338 GLU cc_start: 0.8364 (tt0) cc_final: 0.7967 (mp0)
REVERT: D  325 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7654 (tp)
REVERT: C  372 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8173 (mt-10)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.4479
  time to fit residues: 18.9063
Evaluate side-chains
  43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  331 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  345 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.103008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.078818 restraints weight = 3733.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 3.06
r_work: 0.3386 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2740  Z= 0.123
  Angle     :  0.556   6.739   3660  Z= 0.287
  Chirality :  0.047   0.121    410
  Planarity :  0.002   0.015    465
  Dihedral  :  4.909  14.643    360
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 25.48 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.27 (0.38), residues: 345
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.011   0.003   TYR E 310 
 PHE   0.001   0.000   PHE A 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2740)
  covalent geometry    : angle       0.55643 ( 3660)
  hydrogen bonds       : bond        0.01962 (   26)
  hydrogen bonds       : angle       4.20455 (   78)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1337.04 seconds
wall clock time: 23 minutes 24.51 seconds (1404.51 seconds total)