Starting phenix.real_space_refine
on Wed Mar 12 16:55:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p6e_13227/03_2025/7p6e_13227.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    5050      2.51       5
     N    1500      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8090
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F, I, J, Q, R
  Time building chain proxies: 3.02, per 1000 atoms: 0.37
  Number of scatterers: 8090
  At special positions: 0
  Unit cell: (182.85, 120.75, 40.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1520      8.00
     N    1500      7.00
     C    5050      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: 1.57
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1900

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 19 sheets defined
      0.0% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'I' and resid 275 through 279
      removed outlier: 6.773A  pdb=" N   GLN A 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   ASN C 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE A 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLN C 276 " --> pdb=" O   ILE Q 277 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   ASN Q 279 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ILE C 278 " --> pdb=" O   ASN Q 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 285 through 287
      removed outlier: 8.761A  pdb=" N   SER E 285 " --> pdb=" O   ASN I 286 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   SER A 285 " --> pdb=" O   ASN E 286 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL C 287 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL Q 287 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 306 through 310
      removed outlier: 6.662A  pdb=" N   GLN E 307 " --> pdb=" O   ILE I 308 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   TYR I 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL E 309 " --> pdb=" O   TYR I 310 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 314 through 315
      removed outlier: 6.094A  pdb=" N   ASP A 314 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ASP C 314 " --> pdb=" O   LEU Q 315 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 318 through 322
      removed outlier: 6.611A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL C 318 " --> pdb=" O   THR Q 319 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   LYS Q 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   SER C 320 " --> pdb=" O   LYS Q 321 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 336 through 341
      removed outlier: 6.410A  pdb=" N   VAL C 337 " --> pdb=" O   GLU Q 338 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   LYS Q 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL C 339 " --> pdb=" O   LYS Q 340 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 377
    Processing sheet with id=AA8, first strand: chain 'J' and resid 275 through 279
      removed outlier: 6.714A  pdb=" N   VAL F 275 " --> pdb=" O   GLN J 276 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ILE J 278 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ILE F 277 " --> pdb=" O   ILE J 278 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLN B 276 " --> pdb=" O   ILE D 277 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   ASN D 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ILE B 278 " --> pdb=" O   ASN D 279 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 285 through 287
      removed outlier: 8.703A  pdb=" N   SER F 285 " --> pdb=" O   ASN J 286 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   SER B 285 " --> pdb=" O   ASN F 286 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL D 287 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL R 287 " --> pdb=" O   ASN D 286 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 306 through 310
      removed outlier: 6.698A  pdb=" N   GLN F 307 " --> pdb=" O   ILE J 308 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   TYR J 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL F 309 " --> pdb=" O   TYR J 310 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLN B 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   TYR F 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL B 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 314 through 315
      removed outlier: 6.120A  pdb=" N   ASP B 314 " --> pdb=" O   LEU D 315 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASP D 314 " --> pdb=" O   LEU R 315 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 318 through 322
      removed outlier: 6.448A  pdb=" N   THR B 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   CYS F 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LYS B 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   VAL D 318 " --> pdb=" O   THR R 319 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LYS R 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   SER D 320 " --> pdb=" O   LYS R 321 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 336 through 341
      removed outlier: 6.301A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   VAL D 337 " --> pdb=" O   GLU R 338 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   LYS R 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL D 339 " --> pdb=" O   LYS R 340 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 351
      removed outlier: 6.140A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL D 350 " --> pdb=" O   GLN R 351 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 376 through 377
      removed outlier: 6.738A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU D 376 " --> pdb=" O   THR R 377 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 351
      removed outlier: 6.173A  pdb=" N   VAL C 350 " --> pdb=" O   GLN Q 351 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351
    Processing sheet with id=AB9, first strand: chain 'F' and resid 350 through 351
    Processing sheet with id=AC1, first strand: chain 'F' and resid 376 through 377

    85 hydrogen bonds defined for protein.
    252 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: 1.97

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2575
        1.33 -     1.45: 675
        1.45 -     1.56: 4920
        1.56 -     1.68: 0
        1.68 -     1.79: 20
  Bond restraints: 8190
  Sorted by residual:
  bond pdb=" CA  ASN J 359 "
       pdb=" CB  ASN J 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.487  0.039 1.76e-02 3.23e+03 4.89e+00
  bond pdb=" CA  ASN D 359 "
       pdb=" CB  ASN D 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.488  0.038 1.76e-02 3.23e+03 4.78e+00
  bond pdb=" CA  ASN E 359 "
       pdb=" CB  ASN E 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.488  0.038 1.76e-02 3.23e+03 4.65e+00
  bond pdb=" CA  ASN A 359 "
       pdb=" CB  ASN A 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.488  0.038 1.76e-02 3.23e+03 4.65e+00
  bond pdb=" CA  ASN Q 359 "
       pdb=" CB  ASN Q 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.488  0.038 1.76e-02 3.23e+03 4.64e+00
  ... (remaining 8185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 9729
        1.39 -     2.77: 975
        2.77 -     4.16: 156
        4.16 -     5.55: 60
        5.55 -     6.93: 20
  Bond angle restraints: 10940
  Sorted by residual:
  angle pdb=" N   ASP B 295 "
        pdb=" CA  ASP B 295 "
        pdb=" C   ASP B 295 "
      ideal   model   delta    sigma   weight residual
     108.13  115.06   -6.93 1.72e+00 3.38e-01 1.63e+01
  angle pdb=" N   ASP E 295 "
        pdb=" CA  ASP E 295 "
        pdb=" C   ASP E 295 "
      ideal   model   delta    sigma   weight residual
     108.13  115.04   -6.91 1.72e+00 3.38e-01 1.62e+01
  angle pdb=" N   ASP I 295 "
        pdb=" CA  ASP I 295 "
        pdb=" C   ASP I 295 "
      ideal   model   delta    sigma   weight residual
     108.13  115.02   -6.89 1.72e+00 3.38e-01 1.60e+01
  angle pdb=" N   ASP R 295 "
        pdb=" CA  ASP R 295 "
        pdb=" C   ASP R 295 "
      ideal   model   delta    sigma   weight residual
     108.13  115.02   -6.89 1.72e+00 3.38e-01 1.60e+01
  angle pdb=" N   ASP A 295 "
        pdb=" CA  ASP A 295 "
        pdb=" C   ASP A 295 "
      ideal   model   delta    sigma   weight residual
     108.13  115.02   -6.89 1.72e+00 3.38e-01 1.60e+01
  ... (remaining 10935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.54: 4200
        7.54 -    15.09: 720
       15.09 -    22.63: 100
       22.63 -    30.17: 40
       30.17 -    37.71: 40
  Dihedral angle restraints: 5100
    sinusoidal: 2160
      harmonic: 2940
  Sorted by residual:
  dihedral pdb=" CA  PRO R 301 "
           pdb=" C   PRO R 301 "
           pdb=" N   GLY R 302 "
           pdb=" CA  GLY R 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  PRO C 301 "
           pdb=" C   PRO C 301 "
           pdb=" N   GLY C 302 "
           pdb=" CA  GLY C 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  PRO A 301 "
           pdb=" C   PRO A 301 "
           pdb=" N   GLY A 302 "
           pdb=" CA  GLY A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 5097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 990
       0.073 -    0.146: 240
       0.146 -    0.220: 10
       0.220 -    0.293: 0
       0.293 -    0.366: 10
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CB  ILE R 360 "
            pdb=" CA  ILE R 360 "
            pdb=" CG1 ILE R 360 "
            pdb=" CG2 ILE R 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CB  ILE J 360 "
            pdb=" CA  ILE J 360 "
            pdb=" CG1 ILE J 360 "
            pdb=" CG2 ILE J 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CB  ILE I 360 "
            pdb=" CA  ILE I 360 "
            pdb=" CG1 ILE I 360 "
            pdb=" CG2 ILE I 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.31e+00
  ... (remaining 1247 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 300 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO E 301 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO E 301 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E 301 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL Q 300 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO Q 301 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 301 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 301 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 300 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO R 301 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO R 301 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 301 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2457
        2.87 -     3.37: 6930
        3.37 -     3.88: 13405
        3.88 -     4.39: 13511
        4.39 -     4.90: 28040
  Nonbonded interactions: 64343
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 295 "
            pdb=" NZ  LYS D 311 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" OD2 ASP J 295 "
            pdb=" NZ  LYS J 311 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" OD2 ASP E 295 "
            pdb=" NZ  LYS E 311 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" OD2 ASP A 295 "
            pdb=" NZ  LYS A 311 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" OD2 ASP Q 295 "
            pdb=" NZ  LYS Q 311 "
     model   vdw
     2.359 3.120
  ... (remaining 64338 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'Q'
  selection = chain 'R'
}

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:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     18.390
  Find NCS groups from input model:        0.160
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
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   0.066   8190  Z= 0.582
  Angle     :  0.957   6.934  10940  Z= 0.533
  Chirality :  0.065   0.366   1250
  Planarity :  0.008   0.057   1390
  Dihedral  :  8.257  37.712   3200
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -4.80 (0.18), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.14), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.004   HIS J 299 
 PHE   0.015   0.006   PHE J 378 
 TYR   0.010   0.006   TYR I 310 
 ARG   0.001   0.000   ARG I 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 1.135 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8174 (ttmt)
REVERT: A  295 ASP cc_start: 0.8838 (p0) cc_final: 0.8510 (p0)
REVERT: B  281 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8352 (ttmt)
REVERT: C  321 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7223 (tmtt)
REVERT: D  321 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7188 (tmtt)
REVERT: E  281 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8429 (ttmt)
REVERT: E  372 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7146 (mp0)
REVERT: F  281 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8370 (ttmt)
REVERT: F  372 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7167 (mp0)
REVERT: I  281 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8559 (tptp)
REVERT: I  321 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7410 (pptt)
REVERT: I  348 ASP cc_start: 0.8625 (t0) cc_final: 0.7856 (p0)
REVERT: I  372 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7246 (mp0)
REVERT: J  281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8663 (ttpt)
REVERT: J  321 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7357 (pptt)
REVERT: J  348 ASP cc_start: 0.8631 (t0) cc_final: 0.7846 (p0)
REVERT: J  372 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6843 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1890
  time to fit residues: 73.6770
Evaluate side-chains
  127 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 78 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 374 HIS
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 ASN
** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 374 HIS
** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 336 GLN
J 374 HIS
Q 286 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.125258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.103286 restraints weight = 14369.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 3.76
r_work: 0.4111 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8190  Z= 0.343
  Angle     :  0.666   8.049  10940  Z= 0.335
  Chirality :  0.051   0.143   1250
  Planarity :  0.005   0.041   1390
  Dihedral  :  5.136  13.079   1060
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  9.79 %
    Favored  : 88.42 %
  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: -4.57 (0.19), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.15), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS C 362 
 PHE   0.013   0.003   PHE A 346 
 TYR   0.026   0.003   TYR I 310 
 ARG   0.003   0.001   ARG A 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8264 (ttmt)
REVERT: B  281 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8287 (ttmt)
REVERT: B  283 ASP cc_start: 0.8002 (t0) cc_final: 0.7582 (t0)
REVERT: B  338 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7141 (tm-30)
REVERT: C  321 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6896 (tmtt)
REVERT: C  362 HIS cc_start: 0.7696 (t-170) cc_final: 0.7160 (t-90)
REVERT: D  338 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: D  349 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7459 (mtt-85)
REVERT: D  362 HIS cc_start: 0.7712 (t-170) cc_final: 0.7219 (t-90)
REVERT: E  281 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8529 (tptp)
REVERT: E  282 LEU cc_start: 0.7879 (tt) cc_final: 0.7679 (tt)
REVERT: E  349 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7552 (mtm-85)
REVERT: E  362 HIS cc_start: 0.7676 (t-90) cc_final: 0.7464 (t70)
REVERT: E  372 GLU cc_start: 0.7854 (mt-10) cc_final: 0.6613 (mp0)
REVERT: F  281 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8497 (tptp)
REVERT: F  349 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7436 (mtm-85)
REVERT: F  362 HIS cc_start: 0.7684 (t-90) cc_final: 0.7287 (t-90)
REVERT: F  372 GLU cc_start: 0.7891 (mt-10) cc_final: 0.6732 (mp0)
REVERT: I  281 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8621 (tptp)
REVERT: I  314 ASP cc_start: 0.8311 (t0) cc_final: 0.8085 (t0)
REVERT: I  348 ASP cc_start: 0.8708 (t0) cc_final: 0.8090 (p0)
REVERT: I  362 HIS cc_start: 0.7499 (t70) cc_final: 0.7011 (t70)
REVERT: J  281 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8644 (tptp)
REVERT: J  314 ASP cc_start: 0.8296 (t0) cc_final: 0.8074 (t0)
REVERT: J  348 ASP cc_start: 0.8743 (t0) cc_final: 0.8100 (p0)
REVERT: J  362 HIS cc_start: 0.7492 (t70) cc_final: 0.7139 (t70)
REVERT: J  372 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6521 (mp0)
REVERT: Q  356 SER cc_start: 0.8513 (m) cc_final: 0.8028 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 186
  average time/residue: 0.1870
  time to fit residues: 47.9325
Evaluate side-chains
  136 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Chi-restraints excluded: chain R residue  291 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 ASN
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 286 ASN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 286 ASN
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 374 HIS
E 351 GLN
F 351 GLN
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.208700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5102 r_free = 0.5102 target = 0.181056 restraints weight = 14613.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.4500 rms_B_bonded: 2.12
r_work: 0.4396 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4279 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8190  Z= 0.270
  Angle     :  0.628   8.302  10940  Z= 0.305
  Chirality :  0.051   0.143   1250
  Planarity :  0.004   0.037   1390
  Dihedral  :  4.847  13.011   1060
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 12.63 %
    Favored  : 84.00 %
  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: -4.29 (0.20), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.015   0.003   PHE J 378 
 TYR   0.018   0.002   TYR I 310 
 ARG   0.002   0.000   ARG Q 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8379 (ttmt)
REVERT: A  338 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: B  281 LYS cc_start: 0.8828 (tmtt) cc_final: 0.8408 (ttpt)
REVERT: B  283 ASP cc_start: 0.8098 (t0) cc_final: 0.7683 (t0)
REVERT: B  338 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: C  283 ASP cc_start: 0.8130 (t0) cc_final: 0.7631 (t0)
REVERT: D  338 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7434 (tm-30)
REVERT: D  349 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7658 (mtt-85)
REVERT: E  338 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: E  349 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7824 (mtm-85)
REVERT: E  372 GLU cc_start: 0.8183 (mt-10) cc_final: 0.6957 (mp0)
REVERT: F  281 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8626 (tptp)
REVERT: F  282 LEU cc_start: 0.8096 (tt) cc_final: 0.7878 (tt)
REVERT: F  338 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: F  349 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7785 (mtm-85)
REVERT: F  372 GLU cc_start: 0.8107 (mt-10) cc_final: 0.6824 (mp0)
REVERT: I  281 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8694 (tptp)
REVERT: I  314 ASP cc_start: 0.8365 (t0) cc_final: 0.8126 (t0)
REVERT: I  348 ASP cc_start: 0.8623 (t0) cc_final: 0.8165 (p0)
REVERT: I  362 HIS cc_start: 0.7585 (t70) cc_final: 0.7265 (t-90)
REVERT: J  281 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8654 (tptp)
REVERT: J  314 ASP cc_start: 0.8339 (t0) cc_final: 0.8083 (t0)
REVERT: J  348 ASP cc_start: 0.8646 (t0) cc_final: 0.8183 (p0)
REVERT: J  362 HIS cc_start: 0.7564 (t70) cc_final: 0.7289 (t-90)
REVERT: J  372 GLU cc_start: 0.7891 (mt-10) cc_final: 0.6812 (mp0)
REVERT: J  379 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.6763 (tmm160)
REVERT: Q  349 ARG cc_start: 0.4955 (mmp-170) cc_final: 0.4734 (mmm160)
REVERT: R  349 ARG cc_start: 0.4902 (mmp-170) cc_final: 0.4684 (mmm160)
  outliers start: 32
  outliers final: 21
  residues processed: 175
  average time/residue: 0.1904
  time to fit residues: 45.7798
Evaluate side-chains
  152 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.131620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.110381 restraints weight = 14467.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4393 rms_B_bonded: 3.81
r_work: 0.4257 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   8190  Z= 0.305
  Angle     :  0.624   7.503  10940  Z= 0.308
  Chirality :  0.051   0.144   1250
  Planarity :  0.003   0.032   1390
  Dihedral  :  4.799  13.206   1060
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.21 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.21 (0.20), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 374 
 PHE   0.017   0.003   PHE J 378 
 TYR   0.021   0.003   TYR Q 310 
 ARG   0.002   0.000   ARG Q 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 LYS cc_start: 0.8821 (tmtt) cc_final: 0.8376 (ttmt)
REVERT: A  283 ASP cc_start: 0.8274 (t0) cc_final: 0.8001 (t0)
REVERT: A  338 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: B  281 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8349 (ttmt)
REVERT: B  283 ASP cc_start: 0.8127 (t0) cc_final: 0.7675 (t0)
REVERT: B  338 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: C  307 GLN cc_start: 0.9118 (tt0) cc_final: 0.8918 (tt0)
REVERT: D  283 ASP cc_start: 0.7865 (t0) cc_final: 0.7621 (t0)
REVERT: D  307 GLN cc_start: 0.9127 (tt0) cc_final: 0.8918 (tt0)
REVERT: D  338 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7484 (tm-30)
REVERT: D  349 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7651 (mtt-85)
REVERT: E  281 LYS cc_start: 0.8533 (tptp) cc_final: 0.7885 (ttpt)
REVERT: E  338 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: E  349 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7712 (mtm-85)
REVERT: E  372 GLU cc_start: 0.8028 (mt-10) cc_final: 0.6781 (mp0)
REVERT: F  281 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8579 (tptp)
REVERT: F  338 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7294 (tm-30)
REVERT: F  349 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7612 (mtm-85)
REVERT: F  372 GLU cc_start: 0.7996 (mt-10) cc_final: 0.6749 (mp0)
REVERT: I  281 LYS cc_start: 0.9005 (tmtt) cc_final: 0.8695 (tptp)
REVERT: I  348 ASP cc_start: 0.8625 (t0) cc_final: 0.8095 (p0)
REVERT: I  362 HIS cc_start: 0.7345 (t70) cc_final: 0.7034 (t-90)
REVERT: I  379 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.6754 (tmm160)
REVERT: J  281 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8689 (tptp)
REVERT: J  348 ASP cc_start: 0.8625 (t0) cc_final: 0.8045 (p0)
REVERT: J  362 HIS cc_start: 0.7355 (t70) cc_final: 0.6993 (t-170)
REVERT: J  379 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.6699 (tmm160)
REVERT: Q  307 GLN cc_start: 0.8858 (tt0) cc_final: 0.8630 (tt0)
  outliers start: 30
  outliers final: 25
  residues processed: 166
  average time/residue: 0.1871
  time to fit residues: 42.9327
Evaluate side-chains
  153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Chi-restraints excluded: chain R residue  300 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 58 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0040
   overall best weight:    1.7798

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

Flipped N/Q/H residues before XYZ refinement:
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.214264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5157 r_free = 0.5157 target = 0.185818 restraints weight = 14334.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.4584 rms_B_bonded: 2.09
r_work: 0.4478 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4360 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   8190  Z= 0.182
  Angle     :  0.576   8.394  10940  Z= 0.275
  Chirality :  0.050   0.140   1250
  Planarity :  0.003   0.029   1390
  Dihedral  :  4.437  13.393   1060
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.21 %
    Favored  : 81.37 %
  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: -4.06 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS Q 299 
 PHE   0.015   0.003   PHE A 346 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.001   0.000   ARG J 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8825 (tmtt) cc_final: 0.8352 (ttmt)
REVERT: A  338 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7265 (tm-30)
REVERT: B  281 LYS cc_start: 0.8834 (tmtt) cc_final: 0.8386 (ttmt)
REVERT: B  283 ASP cc_start: 0.8141 (t0) cc_final: 0.7774 (t0)
REVERT: C  338 GLU cc_start: 0.8128 (tt0) cc_final: 0.7202 (tm-30)
REVERT: D  283 ASP cc_start: 0.7846 (t0) cc_final: 0.7550 (t0)
REVERT: D  338 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: D  349 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7381 (mtp85)
REVERT: E  338 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7401 (tm-30)
REVERT: E  349 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7731 (mtm-85)
REVERT: E  372 GLU cc_start: 0.8038 (mt-10) cc_final: 0.6785 (mp0)
REVERT: F  281 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8449 (tptp)
REVERT: F  295 ASP cc_start: 0.9063 (p0) cc_final: 0.8497 (p0)
REVERT: F  338 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: F  349 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7719 (mtm-85)
REVERT: F  372 GLU cc_start: 0.7976 (mt-10) cc_final: 0.6724 (mp0)
REVERT: I  281 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8682 (tptp)
REVERT: I  348 ASP cc_start: 0.8564 (t0) cc_final: 0.8115 (p0)
REVERT: I  362 HIS cc_start: 0.7349 (t70) cc_final: 0.7010 (t-90)
REVERT: I  372 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6645 (mp0)
REVERT: I  378 PHE cc_start: 0.8417 (m-10) cc_final: 0.8175 (m-10)
REVERT: I  379 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.6716 (tmm160)
REVERT: J  348 ASP cc_start: 0.8581 (t0) cc_final: 0.8128 (p0)
REVERT: J  362 HIS cc_start: 0.7338 (t70) cc_final: 0.6971 (t-170)
REVERT: J  372 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6672 (mp0)
REVERT: J  378 PHE cc_start: 0.8609 (m-10) cc_final: 0.8358 (m-10)
REVERT: J  379 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.6704 (tmm160)
  outliers start: 23
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2075
  time to fit residues: 47.0017
Evaluate side-chains
  147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 65 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 93 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0070
   chunk 46 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   overall best weight:    7.2006

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.131106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.110106 restraints weight = 15312.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 3.56
r_work: 0.4216 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   8190  Z= 0.547
  Angle     :  0.733   7.871  10940  Z= 0.382
  Chirality :  0.054   0.147   1250
  Planarity :  0.004   0.046   1390
  Dihedral  :  5.170  14.163   1060
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.95 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.27 (0.20), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.15), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 374 
 PHE   0.019   0.003   PHE A 346 
 TYR   0.017   0.004   TYR I 310 
 ARG   0.005   0.001   ARG R 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8310 (ttmt)
REVERT: B  281 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8320 (ttmt)
REVERT: B  283 ASP cc_start: 0.8211 (t0) cc_final: 0.7952 (t0)
REVERT: C  283 ASP cc_start: 0.8251 (t0) cc_final: 0.8010 (t0)
REVERT: C  307 GLN cc_start: 0.9133 (tt0) cc_final: 0.8860 (tt0)
REVERT: D  338 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7137 (tm-30)
REVERT: D  349 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7458 (mtt-85)
REVERT: E  338 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: E  349 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7737 (mtm-85)
REVERT: E  372 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: F  281 LYS cc_start: 0.8954 (tmtt) cc_final: 0.8506 (tptp)
REVERT: F  283 ASP cc_start: 0.8415 (t0) cc_final: 0.8144 (t0)
REVERT: F  338 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: F  349 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7701 (mtm-85)
REVERT: F  372 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7452 (mt-10)
REVERT: I  281 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8797 (tptp)
REVERT: I  348 ASP cc_start: 0.8887 (t0) cc_final: 0.7943 (p0)
REVERT: I  362 HIS cc_start: 0.7447 (t70) cc_final: 0.7138 (t-90)
REVERT: I  379 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.6759 (tmm160)
REVERT: J  348 ASP cc_start: 0.8882 (t0) cc_final: 0.7946 (p0)
REVERT: J  362 HIS cc_start: 0.7379 (t70) cc_final: 0.7013 (t-170)
REVERT: J  378 PHE cc_start: 0.8736 (m-10) cc_final: 0.8356 (m-10)
REVERT: J  379 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.6681 (tmm160)
  outliers start: 31
  outliers final: 27
  residues processed: 157
  average time/residue: 0.1950
  time to fit residues: 41.6224
Evaluate side-chains
  155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Chi-restraints excluded: chain R residue  300 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 70 optimal weight:    0.0470
   chunk 86 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 82 optimal weight:    0.3980
   chunk 80 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    1.8682

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.212593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5138 r_free = 0.5138 target = 0.182787 restraints weight = 14502.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 2.10
r_work: 0.4448 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4333 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8190  Z= 0.198
  Angle     :  0.599   8.189  10940  Z= 0.292
  Chirality :  0.051   0.139   1250
  Planarity :  0.003   0.024   1390
  Dihedral  :  4.570  14.104   1060
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.21 %
    Favored  : 79.16 %
  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: -4.08 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS Q 299 
 PHE   0.017   0.002   PHE R 378 
 TYR   0.022   0.003   TYR R 310 
 ARG   0.002   0.000   ARG F 379 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8344 (ttmt)
REVERT: B  281 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8350 (ttmt)
REVERT: B  283 ASP cc_start: 0.8169 (t0) cc_final: 0.7939 (t0)
REVERT: C  338 GLU cc_start: 0.8132 (tt0) cc_final: 0.7178 (tm-30)
REVERT: C  349 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7435 (mtp85)
REVERT: D  338 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: E  338 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: E  349 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7809 (mtm-85)
REVERT: E  372 GLU cc_start: 0.7983 (mt-10) cc_final: 0.6717 (mp0)
REVERT: F  281 LYS cc_start: 0.8949 (tmtt) cc_final: 0.8506 (tptp)
REVERT: F  283 ASP cc_start: 0.8430 (t0) cc_final: 0.8206 (t0)
REVERT: F  338 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: F  349 ARG cc_start: 0.8389 (mtp85) cc_final: 0.7815 (mtm-85)
REVERT: F  372 GLU cc_start: 0.7953 (mt-10) cc_final: 0.6692 (mp0)
REVERT: I  281 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8727 (tptp)
REVERT: I  348 ASP cc_start: 0.8615 (t0) cc_final: 0.8069 (p0)
REVERT: I  362 HIS cc_start: 0.7387 (t70) cc_final: 0.7068 (t-90)
REVERT: I  372 GLU cc_start: 0.7948 (mt-10) cc_final: 0.6581 (mp0)
REVERT: I  378 PHE cc_start: 0.8363 (m-10) cc_final: 0.7850 (m-10)
REVERT: I  379 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.6733 (tmm160)
REVERT: J  295 ASP cc_start: 0.9023 (p0) cc_final: 0.8651 (p0)
REVERT: J  348 ASP cc_start: 0.8613 (t0) cc_final: 0.8077 (p0)
REVERT: J  362 HIS cc_start: 0.7387 (t70) cc_final: 0.7040 (t-170)
REVERT: J  372 GLU cc_start: 0.7899 (mt-10) cc_final: 0.6562 (mp0)
REVERT: J  378 PHE cc_start: 0.8560 (m-10) cc_final: 0.8115 (m-10)
REVERT: J  379 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.6681 (tmm160)
  outliers start: 25
  outliers final: 21
  residues processed: 172
  average time/residue: 0.2044
  time to fit residues: 48.1255
Evaluate side-chains
  161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  287 VAL
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0980
   chunk 36 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    4.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.254157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.203379 restraints weight = 15812.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 1.94
r_work: 0.4381 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.4270 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8190  Z= 0.338
  Angle     :  0.632   7.349  10940  Z= 0.320
  Chirality :  0.051   0.138   1250
  Planarity :  0.003   0.027   1390
  Dihedral  :  4.711  13.469   1060
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.42 %
    Favored  : 79.05 %
  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: -4.16 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 374 
 PHE   0.018   0.003   PHE E 346 
 TYR   0.017   0.004   TYR J 310 
 ARG   0.002   0.000   ARG R 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8302 (ttmt)
REVERT: B  281 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8324 (ttmt)
REVERT: B  283 ASP cc_start: 0.8176 (t0) cc_final: 0.7945 (t0)
REVERT: C  349 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7489 (mtp85)
REVERT: D  338 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: E  338 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7310 (tm-30)
REVERT: E  349 ARG cc_start: 0.8374 (mtp85) cc_final: 0.7846 (mtm-85)
REVERT: E  372 GLU cc_start: 0.7919 (mt-10) cc_final: 0.6691 (mp0)
REVERT: F  281 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8551 (tptp)
REVERT: F  283 ASP cc_start: 0.8521 (t0) cc_final: 0.8313 (t0)
REVERT: F  338 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: F  349 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7837 (mtm-85)
REVERT: I  281 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8789 (tptp)
REVERT: I  283 ASP cc_start: 0.8959 (t0) cc_final: 0.8529 (t0)
REVERT: I  348 ASP cc_start: 0.8748 (t0) cc_final: 0.8030 (p0)
REVERT: I  362 HIS cc_start: 0.7447 (t70) cc_final: 0.7107 (t-90)
REVERT: I  379 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.6665 (tmm160)
REVERT: J  348 ASP cc_start: 0.8741 (t0) cc_final: 0.8030 (p0)
REVERT: J  362 HIS cc_start: 0.7460 (t70) cc_final: 0.7117 (t-170)
REVERT: J  379 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.6633 (tmm160)
REVERT: R  349 ARG cc_start: 0.5257 (mmp-170) cc_final: 0.4956 (mmm160)
  outliers start: 24
  outliers final: 23
  residues processed: 154
  average time/residue: 0.1990
  time to fit residues: 41.4879
Evaluate side-chains
  151 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  291 CYS
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.211728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5122 r_free = 0.5122 target = 0.181388 restraints weight = 14756.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.4519 rms_B_bonded: 2.12
r_work: 0.4409 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4293 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8190  Z= 0.214
  Angle     :  0.592   7.124  10940  Z= 0.293
  Chirality :  0.051   0.137   1250
  Planarity :  0.003   0.021   1390
  Dihedral  :  4.515  13.634   1060
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.16 %
    Favored  : 78.53 %
  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: -4.08 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS Q 299 
 PHE   0.014   0.002   PHE E 346 
 TYR   0.023   0.003   TYR Q 310 
 ARG   0.002   0.000   ARG R 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8406 (ttmt)
REVERT: B  281 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8420 (ttmt)
REVERT: C  349 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7621 (mtp85)
REVERT: D  338 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: D  349 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7565 (mtp85)
REVERT: E  338 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: E  349 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7916 (mtm-85)
REVERT: E  372 GLU cc_start: 0.8077 (mt-10) cc_final: 0.6800 (mp0)
REVERT: F  281 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8607 (tptp)
REVERT: F  338 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: F  349 ARG cc_start: 0.8393 (mtp85) cc_final: 0.7910 (mtm-85)
REVERT: F  372 GLU cc_start: 0.8057 (mt-10) cc_final: 0.6766 (mp0)
REVERT: I  281 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8775 (tptp)
REVERT: I  348 ASP cc_start: 0.8607 (t0) cc_final: 0.8130 (p0)
REVERT: I  362 HIS cc_start: 0.7502 (t70) cc_final: 0.7159 (t-90)
REVERT: I  372 GLU cc_start: 0.7993 (mt-10) cc_final: 0.6578 (mp0)
REVERT: I  379 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.6634 (tmm160)
REVERT: J  348 ASP cc_start: 0.8608 (t0) cc_final: 0.8147 (p0)
REVERT: J  362 HIS cc_start: 0.7499 (t70) cc_final: 0.7160 (t-170)
REVERT: J  372 GLU cc_start: 0.7960 (mt-10) cc_final: 0.6565 (mp0)
REVERT: J  379 ARG cc_start: 0.8269 (ttt-90) cc_final: 0.6696 (tmm160)
REVERT: R  349 ARG cc_start: 0.5498 (mmp-170) cc_final: 0.5072 (mmm160)
  outliers start: 22
  outliers final: 21
  residues processed: 163
  average time/residue: 0.1903
  time to fit residues: 42.2877
Evaluate side-chains
  159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  276 GLN
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0270
   chunk 66 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.7242

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.213986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5150 r_free = 0.5150 target = 0.183949 restraints weight = 14557.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4550 rms_B_bonded: 2.09
r_work: 0.4440 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4326 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8190  Z= 0.197
  Angle     :  0.592   7.400  10940  Z= 0.291
  Chirality :  0.051   0.136   1250
  Planarity :  0.003   0.021   1390
  Dihedral  :  4.363  13.382   1060
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.84 %
    Favored  : 78.53 %
  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: -4.05 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS Q 299 
 PHE   0.012   0.002   PHE E 346 
 TYR   0.024   0.003   TYR B 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8350 (ttmt)
REVERT: B  281 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8329 (ttmt)
REVERT: B  283 ASP cc_start: 0.8047 (t0) cc_final: 0.7762 (t0)
REVERT: C  349 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7505 (mtp85)
REVERT: D  338 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: E  338 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7369 (tm-30)
REVERT: E  349 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7910 (mtm-85)
REVERT: E  372 GLU cc_start: 0.7968 (mt-10) cc_final: 0.6666 (mp0)
REVERT: F  310 TYR cc_start: 0.9106 (t80) cc_final: 0.8692 (t80)
REVERT: F  338 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7296 (tm-30)
REVERT: F  349 ARG cc_start: 0.8412 (mtp85) cc_final: 0.7845 (mtm-85)
REVERT: F  372 GLU cc_start: 0.7947 (mt-10) cc_final: 0.6638 (mp0)
REVERT: I  281 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8738 (tptp)
REVERT: I  348 ASP cc_start: 0.8474 (t0) cc_final: 0.8008 (p0)
REVERT: I  362 HIS cc_start: 0.7432 (t70) cc_final: 0.7062 (t-90)
REVERT: I  372 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6451 (mp0)
REVERT: I  378 PHE cc_start: 0.8389 (m-10) cc_final: 0.7948 (m-10)
REVERT: I  379 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.6583 (tmm160)
REVERT: J  348 ASP cc_start: 0.8458 (t0) cc_final: 0.7988 (p0)
REVERT: J  362 HIS cc_start: 0.7395 (t70) cc_final: 0.7068 (t-90)
REVERT: J  372 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6449 (mp0)
REVERT: J  378 PHE cc_start: 0.8457 (m-10) cc_final: 0.7943 (m-10)
REVERT: J  379 ARG cc_start: 0.8227 (ttt-90) cc_final: 0.6645 (tmm160)
REVERT: Q  356 SER cc_start: 0.8573 (m) cc_final: 0.8039 (p)
REVERT: R  349 ARG cc_start: 0.5326 (mmp-170) cc_final: 0.5028 (mmm160)
REVERT: R  356 SER cc_start: 0.8586 (m) cc_final: 0.8038 (p)
  outliers start: 25
  outliers final: 20
  residues processed: 178
  average time/residue: 0.1896
  time to fit residues: 46.4025
Evaluate side-chains
  169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  295 ASP
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  360 ILE
Chi-restraints excluded: chain J residue  287 VAL
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain Q residue  324 SER
Chi-restraints excluded: chain R residue  291 CYS
Chi-restraints excluded: chain R residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0570
   chunk 82 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0870
   chunk 48 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.6280

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

Flipped N/Q/H residues before XYZ refinement:
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.214348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5159 r_free = 0.5159 target = 0.184432 restraints weight = 14650.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.4786 rms_B_bonded: 2.14
r_work: 0.5130 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.5040 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.5040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8190  Z= 0.194
  Angle     :  0.607   8.721  10940  Z= 0.294
  Chirality :  0.051   0.135   1250
  Planarity :  0.003   0.022   1390
  Dihedral  :  4.299  16.599   1060
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.42 %
    Favored  : 77.37 %
  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: -4.02 (0.21), residues: 1010
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.16), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS Q 299 
 PHE   0.014   0.002   PHE E 346 
 TYR   0.030   0.005   TYR B 310 
 ARG   0.002   0.000   ARG F 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3783.69 seconds
wall clock time: 66 minutes 45.62 seconds (4005.62 seconds total)