Starting phenix.real_space_refine
on Wed Mar  5 16:49:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9erm_19926/03_2025/9erm_19926.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       5      5.16       5
     C    1800      2.51       5
     N     530      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.83, per 1000 atoms: 0.99
  Number of scatterers: 2870
  At special positions: 0
  Unit cell: (105.472, 123.6, 32.96, 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       5     16.00
     O     535      8.00
     N     530      7.00
     C    1800      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: 0.63
  Conformation dependent library (CDL) restraints added in 356.7 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 56.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.557A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.822A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.437A  pdb=" N   VAL A 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   LYS D 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER A 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.843A  pdb=" N   GLY C 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ASN A 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.777A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346
      removed outlier: 8.960A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 10.184A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 8.967A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 10.216A  pdb=" N   GLU C 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 9.160A  pdb=" N   SER A 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 9.403A  pdb=" N   LEU C 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL D 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LYS A 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   SER D 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU A 342 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LYS D 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357
      removed outlier: 6.431A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   ILE C 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LYS A 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   SER C 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   GLY A 355 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.472A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.365A  pdb=" N   LYS A 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   THR D 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU A 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 8.483A  pdb=" N   LYS D 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   HIS A 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   THR D 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU A 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310
    Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.437A  pdb=" N   VAL B 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   LYS E 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER B 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 330
      removed outlier: 6.128A  pdb=" N   GLY B 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.777A  pdb=" N   HIS E 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ILE B 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 346
      removed outlier: 6.991A  pdb=" N   GLU B 338 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL E 339 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LYS B 340 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   SER E 341 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   GLU B 342 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LYS E 343 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357
    Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.472A  pdb=" N   THR B 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.365A  pdb=" N   LYS B 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   THR E 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU B 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
      removed outlier: 8.483A  pdb=" N   LYS E 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   HIS B 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   THR E 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU B 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    49 hydrogen bonds defined for protein.
    147 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: 0.67

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 641
        1.33 -     1.45: 563
        1.45 -     1.57: 1706
        1.57 -     1.69: 0
        1.69 -     1.80: 5
  Bond restraints: 2915
  Sorted by residual:
  bond pdb=" C   GLY E 355 "
       pdb=" O   GLY E 355 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 5.30e-03 3.56e+04 5.60e+00
  bond pdb=" C   GLY A 355 "
       pdb=" O   GLY A 355 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.012 5.30e-03 3.56e+04 5.56e+00
  bond pdb=" C   GLY B 355 "
       pdb=" O   GLY B 355 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.012 5.30e-03 3.56e+04 5.51e+00
  bond pdb=" C   GLY C 355 "
       pdb=" O   GLY C 355 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 5.30e-03 3.56e+04 5.44e+00
  bond pdb=" C   GLY D 355 "
       pdb=" O   GLY D 355 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 5.30e-03 3.56e+04 5.42e+00
  ... (remaining 2910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 2986
        1.48 -     2.95: 719
        2.95 -     4.43: 160
        4.43 -     5.90: 15
        5.90 -     7.38: 20
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" C   LEU E 376 "
        pdb=" CA  LEU E 376 "
        pdb=" CB  LEU E 376 "
      ideal   model   delta    sigma   weight residual
     110.14  117.52   -7.38 1.60e+00 3.91e-01 2.13e+01
  angle pdb=" C   LEU D 376 "
        pdb=" CA  LEU D 376 "
        pdb=" CB  LEU D 376 "
      ideal   model   delta    sigma   weight residual
     110.14  117.51   -7.37 1.60e+00 3.91e-01 2.12e+01
  angle pdb=" C   LEU A 376 "
        pdb=" CA  LEU A 376 "
        pdb=" CB  LEU A 376 "
      ideal   model   delta    sigma   weight residual
     110.14  117.49   -7.35 1.60e+00 3.91e-01 2.11e+01
  angle pdb=" C   LEU B 376 "
        pdb=" CA  LEU B 376 "
        pdb=" CB  LEU B 376 "
      ideal   model   delta    sigma   weight residual
     110.14  117.47   -7.33 1.60e+00 3.91e-01 2.10e+01
  angle pdb=" C   LEU C 376 "
        pdb=" CA  LEU C 376 "
        pdb=" CB  LEU C 376 "
      ideal   model   delta    sigma   weight residual
     110.14  117.46   -7.32 1.60e+00 3.91e-01 2.09e+01
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.64: 1510
       10.64 -    21.28: 210
       21.28 -    31.92: 40
       31.92 -    42.56: 5
       42.56 -    53.20: 15
  Dihedral angle restraints: 1780
    sinusoidal: 745
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" CA  ILE E 360 "
           pdb=" C   ILE E 360 "
           pdb=" N   THR E 361 "
           pdb=" CA  THR E 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.76   18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ILE A 360 "
           pdb=" C   ILE A 360 "
           pdb=" N   THR A 361 "
           pdb=" CA  THR A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.77   18.23     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ILE C 360 "
           pdb=" C   ILE C 360 "
           pdb=" N   THR C 361 "
           pdb=" CA  THR C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.77   18.23     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 1777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 170
       0.056 -    0.111: 206
       0.111 -    0.167: 45
       0.167 -    0.223: 14
       0.223 -    0.278: 5
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  LYS C 317 "
            pdb=" N   LYS C 317 "
            pdb=" C   LYS C 317 "
            pdb=" CB  LYS C 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  LYS A 317 "
            pdb=" N   LYS A 317 "
            pdb=" C   LYS A 317 "
            pdb=" CB  LYS A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  LYS E 317 "
            pdb=" N   LYS E 317 "
            pdb=" C   LYS E 317 "
            pdb=" CB  LYS E 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 437 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 370 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.15e+00
        pdb=" C   LYS C 370 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LYS C 370 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE C 371 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 370 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.11e+00
        pdb=" C   LYS A 370 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LYS A 370 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A 371 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 370 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" C   LYS D 370 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LYS D 370 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE D 371 "    0.010 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 1721
        3.09 -     3.54: 2610
        3.54 -     4.00: 4102
        4.00 -     4.45: 4278
        4.45 -     4.90: 8165
  Nonbonded interactions: 20876
  Sorted by model distance:
  nonbonded pdb=" N   ASP C 348 "
            pdb=" O   ASP C 348 "
     model   vdw
     2.641 2.496
  nonbonded pdb=" N   ASP A 348 "
            pdb=" O   ASP A 348 "
     model   vdw
     2.642 2.496
  nonbonded pdb=" N   ASP E 348 "
            pdb=" O   ASP E 348 "
     model   vdw
     2.642 2.496
  nonbonded pdb=" N   ASP B 348 "
            pdb=" O   ASP B 348 "
     model   vdw
     2.642 2.496
  nonbonded pdb=" N   ASP D 348 "
            pdb=" O   ASP D 348 "
     model   vdw
     2.642 2.496
  ... (remaining 20871 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             2.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.670
  Find NCS groups from input model:        0.060
  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:12.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9174
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      :  0.009   0.055   2915  Z= 0.634
  Angle     :  1.427   7.377   3900  Z= 0.908
  Chirality :  0.088   0.278    440
  Planarity :  0.010   0.056    495
  Dihedral  : 11.153  53.196   1120
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  6.06 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.34), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D 374 
 PHE   0.007   0.002   PHE D 378 
 TYR   0.012   0.006   TYR E 310 
 ARG   0.010   0.003   ARG C 349 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.8336 (mt0) cc_final: 0.7876 (tt0)
REVERT: A  317 LYS cc_start: 0.8806 (pttt) cc_final: 0.8524 (ptpp)
REVERT: A  331 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8832 (mtpp)
REVERT: A  340 LYS cc_start: 0.8874 (mtpm) cc_final: 0.8290 (mttm)
REVERT: A  376 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8714 (tp)
REVERT: B  307 GLN cc_start: 0.8600 (mt0) cc_final: 0.8196 (tt0)
REVERT: B  317 LYS cc_start: 0.8897 (pttt) cc_final: 0.8634 (ptpp)
REVERT: B  331 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8949 (mtpp)
REVERT: C  307 GLN cc_start: 0.8628 (mt0) cc_final: 0.8194 (tt0)
REVERT: C  317 LYS cc_start: 0.8902 (pttt) cc_final: 0.8626 (ptpp)
REVERT: C  331 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8950 (mtpp)
REVERT: C  376 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8901 (tp)
REVERT: D  311 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8323 (mttt)
REVERT: D  317 LYS cc_start: 0.8846 (pttt) cc_final: 0.8508 (ptpt)
REVERT: D  331 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8826 (mtpp)
REVERT: D  376 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8819 (tp)
REVERT: E  307 GLN cc_start: 0.8403 (mt0) cc_final: 0.7944 (tt0)
REVERT: E  311 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8426 (mttt)
REVERT: E  317 LYS cc_start: 0.8817 (pttt) cc_final: 0.8479 (ptpt)
REVERT: E  331 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8864 (mtpp)
REVERT: E  376 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8852 (tp)
  outliers start: 10
  outliers final: 1
  residues processed: 152
  average time/residue: 1.4057
  time to fit residues: 217.5542
Evaluate side-chains
  132 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  376 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
A 336 GLN
B 327 ASN
B 336 GLN
C 327 ASN
C 336 GLN
D 327 ASN
D 336 GLN
E 327 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.123054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103279 restraints weight = 3005.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.56
r_work: 0.3356 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9021
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2915  Z= 0.162
  Angle     :  0.592   5.770   3900  Z= 0.293
  Chirality :  0.050   0.134    440
  Planarity :  0.003   0.018    495
  Dihedral  :  6.122  35.248    395
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 13.64 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 374 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.003   0.001   TYR B 310 
 ARG   0.003   0.001   ARG B 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.8036 (mt0) cc_final: 0.7821 (tt0)
REVERT: A  317 LYS cc_start: 0.8555 (pttt) cc_final: 0.8294 (ptpp)
REVERT: A  340 LYS cc_start: 0.8538 (mtpm) cc_final: 0.7821 (mttm)
REVERT: B  307 GLN cc_start: 0.8316 (mt0) cc_final: 0.8102 (tt0)
REVERT: B  317 LYS cc_start: 0.8655 (pttt) cc_final: 0.8389 (ptpp)
REVERT: B  331 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8722 (mtpp)
REVERT: C  307 GLN cc_start: 0.8261 (mt0) cc_final: 0.8005 (tt0)
REVERT: C  317 LYS cc_start: 0.8697 (pttt) cc_final: 0.8434 (ptpp)
REVERT: D  317 LYS cc_start: 0.8624 (pttt) cc_final: 0.8335 (ptpt)
REVERT: E  307 GLN cc_start: 0.7911 (mt0) cc_final: 0.7645 (tt0)
REVERT: E  311 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8308 (mttt)
REVERT: E  317 LYS cc_start: 0.8625 (pttt) cc_final: 0.8310 (ptpt)
REVERT: E  331 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8657 (mtpp)
REVERT: E  340 LYS cc_start: 0.8551 (mtpm) cc_final: 0.7934 (mttm)
  outliers start: 14
  outliers final: 0
  residues processed: 133
  average time/residue: 1.5464
  time to fit residues: 209.1669
Evaluate side-chains
  120 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 330 HIS
B 336 GLN
C 336 GLN
E 336 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.114139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.094112 restraints weight = 3005.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.52
r_work: 0.3216 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9116
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.061   2915  Z= 0.672
  Angle     :  0.873   7.274   3900  Z= 0.434
  Chirality :  0.058   0.158    440
  Planarity :  0.004   0.020    495
  Dihedral  :  5.445  17.008    385
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 18.18 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 374 
 PHE   0.008   0.001   PHE C 378 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.003   0.001   ARG B 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8644 (pttt) cc_final: 0.8322 (ptpp)
REVERT: B  307 GLN cc_start: 0.8387 (mt0) cc_final: 0.8118 (tt0)
REVERT: B  317 LYS cc_start: 0.8740 (pttt) cc_final: 0.8453 (ptpt)
REVERT: B  325 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9071 (tt)
REVERT: B  331 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8745 (mtpp)
REVERT: C  307 GLN cc_start: 0.8351 (mt0) cc_final: 0.8127 (tt0)
REVERT: C  317 LYS cc_start: 0.8781 (pttt) cc_final: 0.8521 (ptpp)
REVERT: D  317 LYS cc_start: 0.8694 (pttt) cc_final: 0.8371 (ptpt)
REVERT: D  369 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8694 (mtmt)
REVERT: E  307 GLN cc_start: 0.8000 (mt0) cc_final: 0.7706 (tt0)
REVERT: E  311 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8337 (mttt)
REVERT: E  317 LYS cc_start: 0.8675 (pttt) cc_final: 0.8280 (ptpt)
REVERT: E  331 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8678 (mtpp)
REVERT: E  340 LYS cc_start: 0.8587 (mtpm) cc_final: 0.7931 (mttm)
  outliers start: 15
  outliers final: 2
  residues processed: 125
  average time/residue: 1.6844
  time to fit residues: 213.9500
Evaluate side-chains
  119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  369 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 336 GLN
C 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.120980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101159 restraints weight = 3033.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.55
r_work: 0.3332 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9055
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2915  Z= 0.173
  Angle     :  0.607   7.798   3900  Z= 0.283
  Chirality :  0.049   0.124    440
  Planarity :  0.002   0.018    495
  Dihedral  :  4.790  16.343    385
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.79 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.03 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 374 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.004   0.001   TYR A 310 
 ARG   0.003   0.001   ARG B 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8558 (pttt) cc_final: 0.8262 (ptpp)
REVERT: A  340 LYS cc_start: 0.8496 (mtpm) cc_final: 0.7768 (mttm)
REVERT: B  317 LYS cc_start: 0.8632 (pttt) cc_final: 0.8354 (ptpp)
REVERT: B  331 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8719 (mtpp)
REVERT: C  317 LYS cc_start: 0.8739 (pttt) cc_final: 0.8482 (ptpp)
REVERT: D  317 LYS cc_start: 0.8614 (pttt) cc_final: 0.8291 (ptpt)
REVERT: D  369 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8701 (mtmt)
REVERT: E  307 GLN cc_start: 0.7909 (mt0) cc_final: 0.7680 (tt0)
REVERT: E  311 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8336 (mttt)
REVERT: E  317 LYS cc_start: 0.8615 (pttt) cc_final: 0.8221 (ptpt)
REVERT: E  331 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8664 (mtpp)
REVERT: E  340 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7913 (mttm)
  outliers start: 10
  outliers final: 2
  residues processed: 120
  average time/residue: 1.7060
  time to fit residues: 207.9692
Evaluate side-chains
  115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  345 ASP
Chi-restraints excluded: chain D residue  369 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0870
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.3764

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

Flipped N/Q/H residues before XYZ refinement:
C 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.119546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.100097 restraints weight = 3012.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.51
r_work: 0.3329 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9058
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2915  Z= 0.176
  Angle     :  0.605   6.694   3900  Z= 0.281
  Chirality :  0.049   0.128    440
  Planarity :  0.003   0.026    495
  Dihedral  :  4.647  16.073    385
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.09 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 374 
 PHE   0.003   0.001   PHE C 378 
 TYR   0.007   0.001   TYR A 310 
 ARG   0.003   0.000   ARG C 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8545 (pttt) cc_final: 0.8250 (ptpp)
REVERT: B  317 LYS cc_start: 0.8594 (pttt) cc_final: 0.8313 (ptpp)
REVERT: B  331 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8729 (mtpp)
REVERT: C  317 LYS cc_start: 0.8723 (pttt) cc_final: 0.8450 (ptpp)
REVERT: D  317 LYS cc_start: 0.8627 (pttt) cc_final: 0.8292 (ptpt)
REVERT: E  311 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8299 (mttt)
REVERT: E  317 LYS cc_start: 0.8650 (pttt) cc_final: 0.8253 (ptpt)
REVERT: E  331 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8668 (mtpp)
REVERT: E  340 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7898 (mttm)
  outliers start: 8
  outliers final: 3
  residues processed: 118
  average time/residue: 1.6834
  time to fit residues: 201.7772
Evaluate side-chains
  110 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  345 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    3.6584

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

Flipped N/Q/H residues before XYZ refinement:
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.116390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.096183 restraints weight = 3037.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.53
r_work: 0.3255 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9098
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2915  Z= 0.368
  Angle     :  0.705   6.769   3900  Z= 0.341
  Chirality :  0.052   0.140    440
  Planarity :  0.003   0.019    495
  Dihedral  :  5.014  16.778    385
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.00 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.99 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 374 
 PHE   0.005   0.001   PHE C 378 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.005   0.001   ARG C 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8581 (pttt) cc_final: 0.8275 (ptpp)
REVERT: B  317 LYS cc_start: 0.8670 (pttt) cc_final: 0.8386 (ptpp)
REVERT: B  325 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9049 (tt)
REVERT: B  331 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8747 (mtpp)
REVERT: C  317 LYS cc_start: 0.8757 (pttt) cc_final: 0.8513 (ptpp)
REVERT: C  325 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8965 (tt)
REVERT: D  317 LYS cc_start: 0.8672 (pttt) cc_final: 0.8343 (ptpt)
REVERT: E  311 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8327 (mttt)
REVERT: E  317 LYS cc_start: 0.8647 (pttt) cc_final: 0.8237 (ptpt)
REVERT: E  331 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8670 (mtpp)
REVERT: E  340 LYS cc_start: 0.8553 (mtpm) cc_final: 0.7901 (mttm)
  outliers start: 7
  outliers final: 2
  residues processed: 116
  average time/residue: 1.7939
  time to fit residues: 211.1636
Evaluate side-chains
  117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 336 GLN
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.118176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097768 restraints weight = 3044.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.56
r_work: 0.3284 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9089
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2915  Z= 0.288
  Angle     :  0.665   8.221   3900  Z= 0.316
  Chirality :  0.050   0.136    440
  Planarity :  0.002   0.013    495
  Dihedral  :  4.899  16.749    385
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.70 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 374 
 PHE   0.005   0.001   PHE D 378 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.005   0.001   ARG A 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8562 (pttt) cc_final: 0.8245 (ptpp)
REVERT: B  317 LYS cc_start: 0.8717 (pttt) cc_final: 0.8427 (ptpp)
REVERT: B  331 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8738 (mtpp)
REVERT: C  317 LYS cc_start: 0.8763 (pttt) cc_final: 0.8504 (ptpp)
REVERT: C  325 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8927 (tt)
REVERT: D  317 LYS cc_start: 0.8663 (pttt) cc_final: 0.8332 (ptpt)
REVERT: E  311 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8325 (mttt)
REVERT: E  317 LYS cc_start: 0.8643 (pttt) cc_final: 0.8276 (ptpt)
REVERT: E  331 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8674 (mtpp)
REVERT: E  340 LYS cc_start: 0.8567 (mtpm) cc_final: 0.7919 (mttm)
  outliers start: 9
  outliers final: 2
  residues processed: 120
  average time/residue: 1.7346
  time to fit residues: 211.3910
Evaluate side-chains
  116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   chunk 24 optimal weight:    8.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 336 GLN
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.118729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.098273 restraints weight = 3040.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.56
r_work: 0.3294 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9086
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2915  Z= 0.256
  Angle     :  0.644   6.120   3900  Z= 0.307
  Chirality :  0.050   0.133    440
  Planarity :  0.002   0.023    495
  Dihedral  :  4.852  16.671    385
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.00 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.97 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 374 
 PHE   0.004   0.001   PHE D 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.004   0.000   ARG A 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8564 (pttt) cc_final: 0.8241 (ptpp)
REVERT: A  340 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7725 (mttm)
REVERT: B  317 LYS cc_start: 0.8679 (pttt) cc_final: 0.8381 (ptpp)
REVERT: B  331 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8738 (mtpp)
REVERT: C  317 LYS cc_start: 0.8761 (pttt) cc_final: 0.8511 (ptpp)
REVERT: C  325 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8930 (tt)
REVERT: C  379 ARG cc_start: 0.7419 (mtp85) cc_final: 0.6634 (mtm110)
REVERT: D  317 LYS cc_start: 0.8643 (pttt) cc_final: 0.8311 (ptpt)
REVERT: E  311 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8321 (mttt)
REVERT: E  317 LYS cc_start: 0.8639 (pttt) cc_final: 0.8268 (ptpt)
REVERT: E  331 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8672 (mtpp)
REVERT: E  340 LYS cc_start: 0.8568 (mtpm) cc_final: 0.7925 (mttm)
  outliers start: 6
  outliers final: 2
  residues processed: 116
  average time/residue: 1.8136
  time to fit residues: 213.5765
Evaluate side-chains
  116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0570
   chunk 16 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6302

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
B 336 GLN
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.123787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.104135 restraints weight = 3019.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.56
r_work: 0.3379 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2915  Z= 0.132
  Angle     :  0.566   6.377   3900  Z= 0.261
  Chirality :  0.048   0.122    440
  Planarity :  0.002   0.014    495
  Dihedral  :  4.383  15.522    385
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.61 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.94 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS C 374 
 PHE   0.003   0.001   PHE A 378 
 TYR   0.006   0.001   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8518 (pttt) cc_final: 0.8178 (ptpt)
REVERT: A  379 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6824 (mtt-85)
REVERT: B  317 LYS cc_start: 0.8601 (pttt) cc_final: 0.8326 (ptpp)
REVERT: B  331 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8733 (mtpp)
REVERT: C  317 LYS cc_start: 0.8729 (pttt) cc_final: 0.8452 (ptpp)
REVERT: D  317 LYS cc_start: 0.8576 (pttt) cc_final: 0.8244 (ptpt)
REVERT: E  311 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8298 (mttt)
REVERT: E  317 LYS cc_start: 0.8592 (pttt) cc_final: 0.8233 (ptpt)
REVERT: E  331 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8662 (mtpp)
REVERT: E  340 LYS cc_start: 0.8563 (mtpm) cc_final: 0.7932 (mttm)
  outliers start: 5
  outliers final: 3
  residues processed: 116
  average time/residue: 1.7227
  time to fit residues: 202.9478
Evaluate side-chains
  115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  369 LYS
Chi-restraints excluded: chain C residue  345 ASP
Chi-restraints excluded: chain D residue  319 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0070
   chunk 7 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   overall best weight:    3.2006

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
B 336 GLN
C 307 GLN
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.116115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.096458 restraints weight = 3077.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.52
r_work: 0.3267 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9091
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2915  Z= 0.328
  Angle     :  0.690   7.234   3900  Z= 0.328
  Chirality :  0.051   0.138    440
  Planarity :  0.002   0.013    495
  Dihedral  :  4.859  16.923    385
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 22.12 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.94 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 374 
 PHE   0.006   0.001   PHE C 378 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.005   0.001   ARG A 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8546 (pttt) cc_final: 0.8222 (ptpp)
REVERT: A  340 LYS cc_start: 0.8468 (mtpp) cc_final: 0.7748 (mttm)
REVERT: B  317 LYS cc_start: 0.8659 (pttt) cc_final: 0.8367 (ptpp)
REVERT: B  331 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8731 (mtpp)
REVERT: C  317 LYS cc_start: 0.8751 (pttt) cc_final: 0.8508 (ptpp)
REVERT: D  317 LYS cc_start: 0.8665 (pttt) cc_final: 0.8331 (ptpt)
REVERT: E  311 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8323 (mttt)
REVERT: E  317 LYS cc_start: 0.8646 (pttt) cc_final: 0.8251 (ptpt)
REVERT: E  331 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8658 (mtpp)
REVERT: E  340 LYS cc_start: 0.8553 (mtpm) cc_final: 0.7907 (mttm)
  outliers start: 2
  outliers final: 1
  residues processed: 112
  average time/residue: 1.7768
  time to fit residues: 201.9971
Evaluate side-chains
  113 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  369 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
B 336 GLN
C 307 GLN
C 336 GLN
E 307 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.118786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.099259 restraints weight = 2980.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.51
r_work: 0.3304 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9067
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2915  Z= 0.210
  Angle     :  0.638   8.110   3900  Z= 0.298
  Chirality :  0.049   0.129    440
  Planarity :  0.002   0.020    495
  Dihedral  :  4.688  16.563    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 21.82 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.93 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 374 
 PHE   0.005   0.001   PHE C 378 
 TYR   0.008   0.002   TYR B 310 
 ARG   0.002   0.000   ARG A 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4396.48 seconds
wall clock time: 75 minutes 22.90 seconds (4522.90 seconds total)