Starting phenix.real_space_refine
on Mon Jan 13 16:55:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h5g_51884/01_2025/9h5g_51884.cif"
  }
  resolution = 2.48
  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       6      5.16       5
     C    2076      2.51       5
     N     600      2.21       5
     O     618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3300
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "B"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "C"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "D"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "E"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "F"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 550
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
  Time building chain proxies: 3.50, per 1000 atoms: 1.06
  Number of scatterers: 3300
  At special positions: 0
  Unit cell: (89.28, 139.128, 33.48, 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       6     16.00
     O     618      8.00
     N     600      7.00
     C    2076      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: 0.77
  Conformation dependent library (CDL) restraints added in 432.7 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 38.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310
      removed outlier: 6.547A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.714A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.555A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.504A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330
      removed outlier: 7.030A  pdb=" N   GLY D 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASN A 327 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   GLY B 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   HIS D 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.662A  pdb=" N   GLN A 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 8.456A  pdb=" N   VAL D 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
      removed outlier: 6.454A  pdb=" N   LYS A 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   PHE D 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356
      removed outlier: 6.802A  pdb=" N   SER D 356 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   ILE B 354 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
      removed outlier: 6.685A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.722A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 375
      removed outlier: 6.598A  pdb=" N   HIS B 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 310
    Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 322
    Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 330
      removed outlier: 5.951A  pdb=" N   GLY C 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.655A  pdb=" N   HIS E 329 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE C 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   GLY E 326 " --> pdb=" O   ASN F 327 " (cutoff:3.500A)
      removed outlier: 8.516A  pdb=" N   HIS F 329 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE E 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 339
    Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 346
    Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 356
      removed outlier: 8.404A  pdb=" N   ILE C 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   ILE E 354 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.658A  pdb=" N   ASN C 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   HIS E 362 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   THR C 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ASN E 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   HIS F 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   THR E 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371
      removed outlier: 6.654A  pdb=" N   LYS C 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LYS E 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 375
      removed outlier: 6.560A  pdb=" N   HIS C 374 " --> pdb=" O   LYS E 375 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   HIS E 374 " --> pdb=" O   LYS F 375 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2

    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: 0.78

  Time building geometry restraints manager: 0.92 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: 857
        1.33 -     1.45: 476
        1.45 -     1.57: 2015
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3354
  Sorted by residual:
  bond pdb=" CZ  ARG F 349 "
       pdb=" NH2 ARG F 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.56e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.41e+00
  bond pdb=" CZ  ARG A 349 "
       pdb=" NH2 ARG A 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.31e+00
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.12e+00
  bond pdb=" CZ  ARG C 349 "
       pdb=" NH2 ARG C 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.55e+00
  ... (remaining 3349 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 2223
        1.29 -     2.59: 1415
        2.59 -     3.88: 613
        3.88 -     5.18: 180
        5.18 -     6.47: 57
  Bond angle restraints: 4488
  Sorted by residual:
  angle pdb=" CA  PHE B 346 "
        pdb=" CB  PHE B 346 "
        pdb=" CG  PHE B 346 "
      ideal   model   delta    sigma   weight residual
     113.80  120.20   -6.40 1.00e+00 1.00e+00 4.10e+01
  angle pdb=" CA  PHE C 346 "
        pdb=" CB  PHE C 346 "
        pdb=" CG  PHE C 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.78   -5.98 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  PHE D 346 "
        pdb=" CB  PHE D 346 "
        pdb=" CG  PHE D 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.68   -5.88 1.00e+00 1.00e+00 3.46e+01
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.57   -5.77 1.00e+00 1.00e+00 3.33e+01
  angle pdb=" CA  PHE F 346 "
        pdb=" CB  PHE F 346 "
        pdb=" CG  PHE F 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.09   -5.29 1.00e+00 1.00e+00 2.80e+01
  ... (remaining 4483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.00: 1694
       10.00 -    20.01: 275
       20.01 -    30.01: 39
       30.01 -    40.01: 18
       40.01 -    50.01: 14
  Dihedral angle restraints: 2040
    sinusoidal: 852
      harmonic: 1188
  Sorted by residual:
  dihedral pdb=" CA  VAL D 318 "
           pdb=" C   VAL D 318 "
           pdb=" N   THR D 319 "
           pdb=" CA  THR D 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.00  -20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  VAL A 318 "
           pdb=" C   VAL A 318 "
           pdb=" N   THR A 319 "
           pdb=" CA  THR A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLN B 351 "
           pdb=" C   GLN B 351 "
           pdb=" N   SER B 352 "
           pdb=" CA  SER B 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.07  -18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 2037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 191
       0.050 -    0.101: 201
       0.101 -    0.151: 69
       0.151 -    0.201: 28
       0.201 -    0.251: 15
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  ARG C 349 "
            pdb=" N   ARG C 349 "
            pdb=" C   ARG C 349 "
            pdb=" CB  ARG C 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  LYS F 347 "
            pdb=" N   LYS F 347 "
            pdb=" C   LYS F 347 "
            pdb=" CB  LYS F 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  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    2.75   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 501 not shown)

  Planarity restraints: 570
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.089 2.00e-02 2.50e+03   4.62e-02 4.26e+01
        pdb=" CG  TYR F 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.081 2.00e-02 2.50e+03   4.37e-02 3.82e+01
        pdb=" CG  TYR E 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.066 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "   -0.074 2.00e-02 2.50e+03   3.82e-02 2.92e+01
        pdb=" CG  TYR A 310 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "   -0.050 2.00e-02 2.50e+03
  ... (remaining 567 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1622
        3.02 -     3.49: 2671
        3.49 -     3.96: 5213
        3.96 -     4.43: 5199
        4.43 -     4.90: 10228
  Nonbonded interactions: 24933
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.551 3.040
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.563 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.576 3.040
  ... (remaining 24928 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             2.610
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:12.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
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      :  0.012   0.036   3354  Z= 0.808
  Angle     :  1.988   6.474   4488  Z= 1.309
  Chirality :  0.088   0.251    504
  Planarity :  0.011   0.046    570
  Dihedral  : 10.879  50.013   1284
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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: -1.90 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.005   HIS E 362 
 PHE   0.031   0.011   PHE A 378 
 TYR   0.089   0.030   TYR F 310 
 ARG   0.006   0.002   ARG F 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.413 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 1.6266
  time to fit residues: 172.5646
Evaluate side-chains
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   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 351 GLN
C 351 GLN
C 368 ASN
F 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.166956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.135877 restraints weight = 3357.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 1.89
r_work: 0.3761 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3653 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3354  Z= 0.249
  Angle     :  0.793  10.366   4488  Z= 0.395
  Chirality :  0.050   0.160    504
  Planarity :  0.003   0.018    570
  Dihedral  :  6.387  17.451    438
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 13.23 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.37 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 362 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.013   0.003   TYR B 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8358 (mmtp) cc_final: 0.7933 (mmtm)
REVERT: A  343 LYS cc_start: 0.8340 (mttt) cc_final: 0.8040 (mttm)
REVERT: A  351 GLN cc_start: 0.7778 (tt0) cc_final: 0.7468 (mt0)
REVERT: B  342 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6753 (mp0)
REVERT: C  325 LEU cc_start: 0.7984 (tp) cc_final: 0.7779 (tt)
REVERT: C  340 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7903 (mmtt)
REVERT: D  340 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7914 (mmtm)
REVERT: E  343 LYS cc_start: 0.8290 (mttt) cc_final: 0.8002 (mttm)
  outliers start: 19
  outliers final: 7
  residues processed: 96
  average time/residue: 1.6361
  time to fit residues: 160.3493
Evaluate side-chains
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  331 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0980
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0870
   chunk 16 optimal weight:    0.0270
   overall best weight:    1.0420

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.172178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.141749 restraints weight = 3314.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.88
r_work: 0.3839 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3354  Z= 0.141
  Angle     :  0.627   8.920   4488  Z= 0.305
  Chirality :  0.049   0.137    504
  Planarity :  0.003   0.019    570
  Dihedral  :  5.381  14.415    438
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 15.34 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.35 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.007   0.002   TYR E 310 
 ARG   0.000   0.000   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8357 (mmtp) cc_final: 0.7936 (mmtm)
REVERT: A  343 LYS cc_start: 0.8401 (mttt) cc_final: 0.8092 (mttm)
REVERT: A  351 GLN cc_start: 0.7594 (tt0) cc_final: 0.7359 (mt0)
REVERT: B  342 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6736 (mp0)
REVERT: C  340 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7763 (mmtm)
REVERT: C  342 GLU cc_start: 0.7889 (mm-30) cc_final: 0.6706 (mp0)
REVERT: D  340 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7877 (mmtm)
REVERT: E  343 LYS cc_start: 0.8261 (mttt) cc_final: 0.7971 (mttm)
REVERT: E  351 GLN cc_start: 0.7499 (tt0) cc_final: 0.7265 (mt0)
  outliers start: 17
  outliers final: 6
  residues processed: 90
  average time/residue: 1.6867
  time to fit residues: 154.8651
Evaluate side-chains
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  320 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
D 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.163477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.132861 restraints weight = 3359.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.87
r_work: 0.3719 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3354  Z= 0.317
  Angle     :  0.789   9.699   4488  Z= 0.388
  Chirality :  0.051   0.158    504
  Planarity :  0.004   0.028    570
  Dihedral  :  6.183  18.377    438
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 14.81 %
    Favored  : 79.10 %
  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: -2.66 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 362 
 PHE   0.008   0.002   PHE C 378 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8086 (mmtm)
REVERT: A  343 LYS cc_start: 0.8244 (mttt) cc_final: 0.7949 (mttm)
REVERT: A  351 GLN cc_start: 0.7787 (tt0) cc_final: 0.7559 (mt0)
REVERT: B  342 GLU cc_start: 0.7933 (mm-30) cc_final: 0.6781 (mp0)
REVERT: B  351 GLN cc_start: 0.8135 (tt0) cc_final: 0.7794 (mt0)
REVERT: C  340 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7880 (mmtt)
REVERT: F  340 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8048 (mmtm)
REVERT: F  351 GLN cc_start: 0.7792 (tt0) cc_final: 0.7491 (mt0)
  outliers start: 23
  outliers final: 12
  residues processed: 90
  average time/residue: 1.5863
  time to fit residues: 145.8536
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   overall best weight:    5.3388

-------------------------------------------------------------------------------
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 = 0.4219 r_free = 0.4219 target = 0.161902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.131133 restraints weight = 3327.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.85
r_work: 0.3697 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3354  Z= 0.398
  Angle     :  0.848   9.648   4488  Z= 0.417
  Chirality :  0.052   0.169    504
  Planarity :  0.004   0.034    570
  Dihedral  :  6.452  18.412    438
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 15.08 %
    Favored  : 79.10 %
  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: -2.85 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 362 
 PHE   0.010   0.003   PHE C 378 
 TYR   0.015   0.004   TYR F 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8098 (mmtm)
REVERT: A  343 LYS cc_start: 0.8178 (mttt) cc_final: 0.7488 (tptm)
REVERT: A  351 GLN cc_start: 0.7875 (tt0) cc_final: 0.7616 (mt0)
REVERT: B  340 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8205 (mmtt)
REVERT: B  342 GLU cc_start: 0.7957 (mm-30) cc_final: 0.6750 (mp0)
REVERT: B  351 GLN cc_start: 0.8249 (tt0) cc_final: 0.7959 (mt0)
REVERT: C  340 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7934 (mmtt)
REVERT: C  351 GLN cc_start: 0.8121 (tt0) cc_final: 0.7857 (mt0)
REVERT: D  338 GLU cc_start: 0.8537 (tt0) cc_final: 0.8179 (tm-30)
REVERT: D  343 LYS cc_start: 0.8127 (mttt) cc_final: 0.7871 (mttp)
REVERT: D  351 GLN cc_start: 0.7713 (tt0) cc_final: 0.7438 (mt0)
REVERT: E  343 LYS cc_start: 0.8278 (mttt) cc_final: 0.7984 (mttm)
REVERT: F  340 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8048 (mmtm)
REVERT: F  351 GLN cc_start: 0.7873 (tt0) cc_final: 0.7576 (mt0)
  outliers start: 22
  outliers final: 15
  residues processed: 92
  average time/residue: 1.5721
  time to fit residues: 147.6169
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 18 optimal weight:    0.0000
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    3.5992

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.163266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.132608 restraints weight = 3404.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 1.87
r_work: 0.3716 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3354  Z= 0.283
  Angle     :  0.761  11.245   4488  Z= 0.369
  Chirality :  0.050   0.164    504
  Planarity :  0.004   0.031    570
  Dihedral  :  6.081  16.951    438
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 15.34 %
    Favored  : 78.84 %
  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: -2.79 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.006   0.002   PHE C 378 
 TYR   0.011   0.003   TYR F 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8088 (mmtm)
REVERT: A  343 LYS cc_start: 0.8265 (mttt) cc_final: 0.7564 (tptm)
REVERT: A  351 GLN cc_start: 0.7824 (tt0) cc_final: 0.7610 (mt0)
REVERT: B  340 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8172 (mmtt)
REVERT: B  342 GLU cc_start: 0.7962 (mm-30) cc_final: 0.6762 (mp0)
REVERT: C  325 LEU cc_start: 0.8169 (tp) cc_final: 0.7969 (tt)
REVERT: C  340 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7929 (mmtt)
REVERT: C  351 GLN cc_start: 0.8096 (tt0) cc_final: 0.7886 (mt0)
REVERT: D  338 GLU cc_start: 0.8510 (tt0) cc_final: 0.8153 (tm-30)
REVERT: D  343 LYS cc_start: 0.8116 (mttt) cc_final: 0.7759 (mttm)
REVERT: D  351 GLN cc_start: 0.7707 (tt0) cc_final: 0.7493 (mt0)
REVERT: E  343 LYS cc_start: 0.8280 (mttt) cc_final: 0.8003 (mttm)
REVERT: F  340 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8025 (mmtm)
REVERT: F  351 GLN cc_start: 0.7807 (tt0) cc_final: 0.7558 (mt0)
  outliers start: 22
  outliers final: 13
  residues processed: 93
  average time/residue: 1.6104
  time to fit residues: 152.8385
Evaluate side-chains
  98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   overall best weight:    5.9988

-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.161260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.130514 restraints weight = 3322.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.85
r_work: 0.3690 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   3354  Z= 0.444
  Angle     :  0.874  12.650   4488  Z= 0.428
  Chirality :  0.053   0.186    504
  Planarity :  0.005   0.034    570
  Dihedral  :  6.414  18.102    438
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 15.34 %
    Favored  : 78.57 %
  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: -2.93 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 362 
 PHE   0.010   0.003   PHE C 378 
 TYR   0.015   0.004   TYR F 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8109 (mmtm)
REVERT: A  343 LYS cc_start: 0.8174 (mttt) cc_final: 0.7421 (tptm)
REVERT: A  351 GLN cc_start: 0.7894 (tt0) cc_final: 0.7678 (mt0)
REVERT: B  340 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8208 (mmtt)
REVERT: B  342 GLU cc_start: 0.7974 (mm-30) cc_final: 0.6744 (mp0)
REVERT: C  340 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7945 (mmtt)
REVERT: C  351 GLN cc_start: 0.8105 (tt0) cc_final: 0.7903 (mt0)
REVERT: D  338 GLU cc_start: 0.8510 (tt0) cc_final: 0.8148 (tm-30)
REVERT: D  343 LYS cc_start: 0.8101 (mttt) cc_final: 0.7728 (mttm)
REVERT: D  351 GLN cc_start: 0.7736 (tt0) cc_final: 0.7490 (mt0)
REVERT: E  343 LYS cc_start: 0.8287 (mttt) cc_final: 0.7980 (mttm)
REVERT: F  340 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8062 (mmtm)
REVERT: F  343 LYS cc_start: 0.8066 (mttt) cc_final: 0.7665 (mttm)
REVERT: F  351 GLN cc_start: 0.7811 (tt0) cc_final: 0.7561 (mt0)
  outliers start: 23
  outliers final: 13
  residues processed: 99
  average time/residue: 1.6828
  time to fit residues: 169.8126
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.0040
   chunk 24 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    2.1196

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.166101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.135157 restraints weight = 3281.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 1.87
r_work: 0.3752 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3354  Z= 0.193
  Angle     :  0.710  12.301   4488  Z= 0.334
  Chirality :  0.050   0.180    504
  Planarity :  0.004   0.031    570
  Dihedral  :  5.659  15.512    438
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.72 %
    Favored  : 76.72 %
  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: -2.71 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.004   0.001   PHE C 378 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.000   0.000   ARG A 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8427 (mmtp) cc_final: 0.8080 (mmtm)
REVERT: A  343 LYS cc_start: 0.8298 (mttt) cc_final: 0.7611 (tptm)
REVERT: B  340 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8100 (mmtt)
REVERT: B  342 GLU cc_start: 0.7944 (mm-30) cc_final: 0.6732 (mp0)
REVERT: C  340 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7882 (mmtm)
REVERT: D  343 LYS cc_start: 0.8099 (mttt) cc_final: 0.7762 (mttm)
REVERT: E  343 LYS cc_start: 0.8262 (mttt) cc_final: 0.8000 (mttm)
REVERT: F  340 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7986 (mmtm)
  outliers start: 21
  outliers final: 13
  residues processed: 92
  average time/residue: 1.6358
  time to fit residues: 153.5802
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain C residue  353 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.162974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.131872 restraints weight = 3330.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 1.88
r_work: 0.3708 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3354  Z= 0.325
  Angle     :  0.824  14.003   4488  Z= 0.389
  Chirality :  0.052   0.204    504
  Planarity :  0.004   0.032    570
  Dihedral  :  6.002  17.099    438
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 19.05 %
    Favored  : 75.93 %
  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: -2.83 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.007   0.002   PHE C 378 
 TYR   0.012   0.003   TYR B 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8067 (mmtm)
REVERT: A  343 LYS cc_start: 0.8219 (mttt) cc_final: 0.7450 (tptm)
REVERT: B  340 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8145 (mmtt)
REVERT: B  342 GLU cc_start: 0.7974 (mm-30) cc_final: 0.6776 (mp0)
REVERT: C  340 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7949 (mmtt)
REVERT: D  340 LYS cc_start: 0.8435 (mttm) cc_final: 0.8224 (mmtp)
REVERT: E  343 LYS cc_start: 0.8260 (mttt) cc_final: 0.7978 (mttm)
REVERT: F  340 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8070 (mmtm)
  outliers start: 19
  outliers final: 15
  residues processed: 89
  average time/residue: 1.5570
  time to fit residues: 141.6900
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.165074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.134015 restraints weight = 3266.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.87
r_work: 0.3737 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3354  Z= 0.230
  Angle     :  0.769  14.573   4488  Z= 0.355
  Chirality :  0.051   0.212    504
  Planarity :  0.004   0.032    570
  Dihedral  :  5.717  16.031    438
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.58 %
    Favored  : 76.46 %
  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: -2.72 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.005   0.001   PHE C 378 
 TYR   0.009   0.002   TYR B 310 
 ARG   0.000   0.000   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  340 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8051 (mmtm)
REVERT: A  343 LYS cc_start: 0.8268 (mttt) cc_final: 0.7566 (tptm)
REVERT: B  340 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8109 (mmtt)
REVERT: B  342 GLU cc_start: 0.7953 (mm-30) cc_final: 0.6724 (mp0)
REVERT: C  340 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7908 (mmtt)
REVERT: D  340 LYS cc_start: 0.8414 (mttm) cc_final: 0.8206 (mmtp)
REVERT: E  343 LYS cc_start: 0.8255 (mttt) cc_final: 0.7978 (mttm)
REVERT: F  340 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8013 (mmtm)
  outliers start: 15
  outliers final: 13
  residues processed: 85
  average time/residue: 1.5584
  time to fit residues: 135.3616
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  331 LYS
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  340 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.163165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.132113 restraints weight = 3277.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 1.87
r_work: 0.3715 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3354  Z= 0.323
  Angle     :  0.829  14.504   4488  Z= 0.390
  Chirality :  0.052   0.211    504
  Planarity :  0.004   0.032    570
  Dihedral  :  5.984  16.900    438
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.31 %
    Favored  : 75.93 %
  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: -2.79 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.007   0.002   PHE C 378 
 TYR   0.012   0.003   TYR B 310 
 ARG   0.001   0.000   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3945.16 seconds
wall clock time: 71 minutes 35.59 seconds (4295.59 seconds total)