Starting phenix.real_space_refine
on Sat May 10 16:01:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gzz_34406/05_2025/8gzz_34406.cif"
  }
  resolution = 3.52
  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=  -0.003 sd=   0.027
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      36      5.16       5
     C    4186      2.51       5
     N    1084      2.21       5
     O    1262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6568
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1558
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
    Chain: "D"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 824
          Classifications: {'peptide': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 902
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "F"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 824
          Classifications: {'peptide': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104}
    Chain: "G"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 902
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
  Time building chain proxies: 6.36, per 1000 atoms: 0.97
  Number of scatterers: 6568
  At special positions: 0
  Unit cell: (87.36, 130.624, 79.04, 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      36     16.00
     O    1262      8.00
     N    1084      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  35 " - pdb=" SG  CYS E  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  21 " - pdb=" SG  CYS G  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  35 " - pdb=" SG  CYS G  50 " distance=2.03

  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: 1.50
  Conformation dependent library (CDL) restraints added in 947.8 milliseconds
  

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 17 sheets defined
      9.6% alpha, 27.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.523A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.914A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 4.056A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.508A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 506
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.868A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'E' and resid 63 through 66
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.092A  pdb=" N   THR E  91 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 66
    Processing helix  chain 'G' and resid 87 through 91
      removed outlier: 3.981A  pdb=" N   THR G  91 " --> pdb=" O   ALA G  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.572A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.805A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.575A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.741A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.609A  pdb=" N   GLU D  13 " --> pdb=" O   VAL D 108 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6
      removed outlier: 3.717A  pdb=" N   THR E  20 " --> pdb=" O   SER E   6 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 61
      removed outlier: 3.576A  pdb=" N   CYS E  50 " --> pdb=" O   TYR E  60 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TRP E  36 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   MET E  34 " --> pdb=" O   CYS E  50 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASP E  33 " --> pdb=" O   ASP E  99 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU E 111 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61
      removed outlier: 3.576A  pdb=" N   CYS E  50 " --> pdb=" O   TYR E  60 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TRP E  36 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   MET E  34 " --> pdb=" O   CYS E  50 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASP E  33 " --> pdb=" O   ASP E  99 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7
    Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13
      removed outlier: 3.668A  pdb=" N   GLU F  13 " --> pdb=" O   VAL F 108 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 6
      removed outlier: 3.738A  pdb=" N   THR G  20 " --> pdb=" O   SER G   6 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 60 through 61
      removed outlier: 6.646A  pdb=" N   TRP G  36 " --> pdb=" O   ILE G  48 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   CYS G  50 " --> pdb=" O   MET G  34 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   MET G  34 " --> pdb=" O   CYS G  50 " (cutoff:3.500A)

    197 hydrogen bonds defined for protein.
    459 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: 1.95

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2082
        1.34 -     1.47: 1820
        1.47 -     1.59: 2798
        1.59 -     1.71: 0
        1.71 -     1.83: 42
  Bond restraints: 6742
  Sorted by residual:
  bond pdb=" C   LYS A 356 "
       pdb=" N   ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.372 -0.042 1.32e-02 5.74e+03 1.02e+01
  bond pdb=" C   GLN F  24 "
       pdb=" N   ALA F  25 "
    ideal  model  delta    sigma   weight residual
    1.329  1.285  0.044 1.44e-02 4.82e+03 9.46e+00
  bond pdb=" C   CYS F  23 "
       pdb=" N   GLN F  24 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.44e-02 4.82e+03 7.41e+00
  bond pdb=" N   GLN F  24 "
       pdb=" CA  GLN F  24 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.23e-02 6.61e+03 6.89e+00
  bond pdb=" N   TYR A 449 "
       pdb=" CA  TYR A 449 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.08e-02 8.57e+03 6.79e+00
  ... (remaining 6737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 8628
        1.15 -     2.31: 435
        2.31 -     3.46: 91
        3.46 -     4.62: 24
        4.62 -     5.77: 6
  Bond angle restraints: 9184
  Sorted by residual:
  angle pdb=" C   TYR F  49 "
        pdb=" CA  TYR F  49 "
        pdb=" CB  TYR F  49 "
      ideal   model   delta    sigma   weight residual
     109.80  115.57   -5.77 1.65e+00 3.67e-01 1.22e+01
  angle pdb=" C   LYS A 356 "
        pdb=" N   ARG A 357 "
        pdb=" CA  ARG A 357 "
      ideal   model   delta    sigma   weight residual
     123.00  118.33    4.67 1.38e+00 5.25e-01 1.15e+01
  angle pdb=" CA  GLN A 414 "
        pdb=" C   GLN A 414 "
        pdb=" O   GLN A 414 "
      ideal   model   delta    sigma   weight residual
     121.56  118.05    3.51 1.09e+00 8.42e-01 1.04e+01
  angle pdb=" N   TYR F  49 "
        pdb=" CA  TYR F  49 "
        pdb=" C   TYR F  49 "
      ideal   model   delta    sigma   weight residual
     110.42  105.78    4.64 1.55e+00 4.16e-01 8.96e+00
  angle pdb=" N   PHE A 377 "
        pdb=" CA  PHE A 377 "
        pdb=" C   PHE A 377 "
      ideal   model   delta    sigma   weight residual
     112.72  109.48    3.24 1.14e+00 7.69e-01 8.09e+00
  ... (remaining 9179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 3617
       17.80 -    35.61: 289
       35.61 -    53.41: 29
       53.41 -    71.22: 7
       71.22 -    89.02: 4
  Dihedral angle restraints: 3946
    sinusoidal: 1490
      harmonic: 2456
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   24.54   68.46     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   26.66   66.34     1      1.00e+01 1.00e-02 5.75e+01
  dihedral pdb=" CA  CYS A 379 "
           pdb=" C   CYS A 379 "
           pdb=" N   TYR A 380 "
           pdb=" CA  TYR A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.72  -18.28     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 529
       0.030 -    0.059: 314
       0.059 -    0.089: 88
       0.089 -    0.118: 57
       0.118 -    0.148: 12
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" CA  ILE F  21 "
            pdb=" N   ILE F  21 "
            pdb=" C   ILE F  21 "
            pdb=" CB  ILE F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  GLN F  24 "
            pdb=" N   GLN F  24 "
            pdb=" C   GLN F  24 "
            pdb=" CB  GLN F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  GLU B 465 "
            pdb=" N   GLU B 465 "
            pdb=" C   GLU B 465 "
            pdb=" CB  GLU B 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 997 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F  48 "   -0.007 2.00e-02 2.50e+03   1.54e-02 2.36e+00
        pdb=" C   ILE F  48 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE F  48 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR F  49 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F  24 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.21e+00
        pdb=" C   GLN F  24 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLN F  24 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA F  25 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  49 "   -0.012 2.00e-02 2.50e+03   9.52e-03 1.81e+00
        pdb=" CG  TYR D  49 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR D  49 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1441
        2.78 -     3.31: 5887
        3.31 -     3.84: 10276
        3.84 -     4.37: 12188
        4.37 -     4.90: 21752
  Nonbonded interactions: 51544
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 442 "
            pdb=" OH  TYR G 103 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   SER E  29 "
            pdb=" OG1 THR E  53 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   SER G  29 "
            pdb=" OG1 THR G  53 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" NE2 GLN F  90 "
            pdb=" O   SER F  93 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OD2 ASP A 364 "
            pdb=" OG  SER A 366 "
     model   vdw
     2.340 3.040
  ... (remaining 51539 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.920
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.690
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.004   0.044   6756  Z= 0.227
  Angle     :  0.621   5.770   9212  Z= 0.362
  Chirality :  0.044   0.148   1000
  Planarity :  0.003   0.028   1184
  Dihedral  : 12.188  89.023   2348
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.99 (0.28), residues: 842
  helix: -3.59 (0.49), residues: 54
  sheet:  0.41 (0.33), residues: 264
  loop : -0.90 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.021   0.002   PHE A 347 
 TYR   0.023   0.001   TYR D  49 
 ARG   0.002   0.000   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18472 (  186)
  hydrogen bonds       : angle       8.99483 (  459)
  SS BOND              : bond        0.00294 (   14)
  SS BOND              : angle       1.03895 (   28)
  covalent geometry    : bond        0.00437 ( 6742)
  covalent geometry    : angle       0.61966 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1969
  time to fit residues: 28.9697
Evaluate side-chains
  93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0050
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
D  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.084368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.070277 restraints weight = 16509.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.072935 restraints weight = 7962.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.074648 restraints weight = 5085.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6756  Z= 0.136
  Angle     :  0.540   4.999   9212  Z= 0.290
  Chirality :  0.043   0.145   1000
  Planarity :  0.004   0.040   1184
  Dihedral  :  4.186  16.306    932
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  7.89 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.29), residues: 842
  helix: -3.92 (0.42), residues: 54
  sheet:  0.24 (0.32), residues: 292
  loop : -0.89 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.045   0.001   PHE B 374 
 TYR   0.011   0.001   TYR A 380 
 ARG   0.005   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  186)
  hydrogen bonds       : angle       6.78562 (  459)
  SS BOND              : bond        0.00384 (   14)
  SS BOND              : angle       1.20693 (   28)
  covalent geometry    : bond        0.00302 ( 6742)
  covalent geometry    : angle       0.53668 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8592 (m-30) cc_final: 0.8345 (t0)
REVERT: D   82 ASP cc_start: 0.7530 (m-30) cc_final: 0.7084 (m-30)
REVERT: D   96 ASP cc_start: 0.8085 (p0) cc_final: 0.7181 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 102
  average time/residue: 0.1846
  time to fit residues: 25.0861
Evaluate side-chains
  96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 14 optimal weight:    0.3980
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0040
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.084428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.070157 restraints weight = 16604.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.072829 restraints weight = 8039.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.074552 restraints weight = 5143.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6756  Z= 0.120
  Angle     :  0.500   4.600   9212  Z= 0.267
  Chirality :  0.042   0.141   1000
  Planarity :  0.004   0.034   1184
  Dihedral  :  4.075  15.278    932
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  9.86 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.29), residues: 842
  helix: -4.04 (0.41), residues: 54
  sheet:  0.33 (0.32), residues: 282
  loop : -0.85 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.009   0.001   PHE A 347 
 TYR   0.012   0.001   TYR A 380 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03117 (  186)
  hydrogen bonds       : angle       6.27920 (  459)
  SS BOND              : bond        0.00391 (   14)
  SS BOND              : angle       1.08653 (   28)
  covalent geometry    : bond        0.00275 ( 6742)
  covalent geometry    : angle       0.49712 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: B  376 THR cc_start: 0.8674 (m) cc_final: 0.8087 (p)
REVERT: B  420 ASP cc_start: 0.8584 (m-30) cc_final: 0.8322 (t0)
REVERT: D   96 ASP cc_start: 0.8093 (p0) cc_final: 0.7167 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1862
  time to fit residues: 25.9274
Evaluate side-chains
  101 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0050
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3359 r_free = 0.3359 target = 0.083334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.069408 restraints weight = 16747.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.072049 restraints weight = 7984.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073754 restraints weight = 5049.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.147
  Angle     :  0.507   5.988   9212  Z= 0.273
  Chirality :  0.042   0.136   1000
  Planarity :  0.004   0.039   1184
  Dihedral  :  4.103  16.505    932
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.82 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.29), residues: 842
  helix: -4.05 (0.41), residues: 54
  sheet: -0.03 (0.33), residues: 268
  loop : -0.88 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.010   0.001   PHE E  95 
 TYR   0.011   0.001   TYR A 380 
 ARG   0.003   0.000   ARG D  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02846 (  186)
  hydrogen bonds       : angle       6.15230 (  459)
  SS BOND              : bond        0.00510 (   14)
  SS BOND              : angle       1.07511 (   28)
  covalent geometry    : bond        0.00334 ( 6742)
  covalent geometry    : angle       0.50405 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8295 (t0)
REVERT: D   96 ASP cc_start: 0.8109 (p0) cc_final: 0.7218 (p0)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1723
  time to fit residues: 23.6340
Evaluate side-chains
  102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0570
   chunk 15 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.067655 restraints weight = 16661.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.070287 restraints weight = 7973.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.071979 restraints weight = 5081.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6756  Z= 0.130
  Angle     :  0.494   5.318   9212  Z= 0.264
  Chirality :  0.042   0.139   1000
  Planarity :  0.004   0.047   1184
  Dihedral  :  4.037  15.868    932
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.66 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.28), residues: 842
  helix: -4.06 (0.41), residues: 54
  sheet: -0.08 (0.32), residues: 270
  loop : -0.87 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.008   0.001   PHE E  95 
 TYR   0.009   0.001   TYR D  49 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02664 (  186)
  hydrogen bonds       : angle       6.01132 (  459)
  SS BOND              : bond        0.00319 (   14)
  SS BOND              : angle       1.02702 (   28)
  covalent geometry    : bond        0.00297 ( 6742)
  covalent geometry    : angle       0.49178 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  376 THR cc_start: 0.8682 (m) cc_final: 0.8078 (p)
REVERT: B  420 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (t0)
REVERT: D   96 ASP cc_start: 0.8155 (p0) cc_final: 0.7284 (p0)
  outliers start: 13
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1902
  time to fit residues: 28.0472
Evaluate side-chains
  104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3327 r_free = 0.3327 target = 0.082069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.068170 restraints weight = 16715.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.070765 restraints weight = 7905.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.072436 restraints weight = 4987.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6756  Z= 0.134
  Angle     :  0.502   5.029   9212  Z= 0.270
  Chirality :  0.042   0.137   1000
  Planarity :  0.004   0.049   1184
  Dihedral  :  4.084  15.303    932
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.80 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.28), residues: 842
  helix: -4.16 (0.39), residues: 54
  sheet: -0.07 (0.32), residues: 278
  loop : -0.92 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.009   0.001   PHE E  95 
 TYR   0.009   0.001   TYR A 380 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02676 (  186)
  hydrogen bonds       : angle       5.99095 (  459)
  SS BOND              : bond        0.00394 (   14)
  SS BOND              : angle       1.16749 (   28)
  covalent geometry    : bond        0.00307 ( 6742)
  covalent geometry    : angle       0.49879 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: B  376 THR cc_start: 0.8614 (m) cc_final: 0.7906 (p)
REVERT: B  420 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8306 (t0)
REVERT: B  474 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: D   96 ASP cc_start: 0.8173 (p0) cc_final: 0.7302 (p0)
  outliers start: 17
  outliers final: 10
  residues processed: 113
  average time/residue: 0.2031
  time to fit residues: 31.9957
Evaluate side-chains
  109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 57 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3290 r_free = 0.3290 target = 0.080540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.066357 restraints weight = 16794.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.068914 restraints weight = 8083.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.070567 restraints weight = 5187.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6756  Z= 0.214
  Angle     :  0.577  11.371   9212  Z= 0.303
  Chirality :  0.044   0.139   1000
  Planarity :  0.004   0.050   1184
  Dihedral  :  4.376  16.777    932
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.65 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.28), residues: 842
  helix: -4.03 (0.42), residues: 54
  sheet: -0.17 (0.32), residues: 278
  loop : -1.01 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.014   0.001   PHE E  95 
 TYR   0.010   0.001   TYR E 103 
 ARG   0.004   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02943 (  186)
  hydrogen bonds       : angle       6.16966 (  459)
  SS BOND              : bond        0.00423 (   14)
  SS BOND              : angle       1.24231 (   28)
  covalent geometry    : bond        0.00491 ( 6742)
  covalent geometry    : angle       0.57333 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8313 (pt0) cc_final: 0.8069 (pt0)
REVERT: B  376 THR cc_start: 0.8798 (m) cc_final: 0.8218 (p)
REVERT: B  420 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (t0)
REVERT: D   96 ASP cc_start: 0.8210 (p0) cc_final: 0.7342 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1814
  time to fit residues: 26.2394
Evaluate side-chains
  102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0980
   chunk 10 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3303 r_free = 0.3303 target = 0.080968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.066735 restraints weight = 16822.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.069291 restraints weight = 8096.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.070966 restraints weight = 5190.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6756  Z= 0.166
  Angle     :  0.550   9.531   9212  Z= 0.292
  Chirality :  0.043   0.138   1000
  Planarity :  0.004   0.045   1184
  Dihedral  :  4.281  16.131    932
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.94 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.28), residues: 842
  helix: -4.01 (0.43), residues: 54
  sheet: -0.24 (0.32), residues: 280
  loop : -1.03 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.012   0.001   PHE B 486 
 TYR   0.009   0.001   TYR D  49 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02708 (  186)
  hydrogen bonds       : angle       6.06431 (  459)
  SS BOND              : bond        0.00388 (   14)
  SS BOND              : angle       1.08412 (   28)
  covalent geometry    : bond        0.00378 ( 6742)
  covalent geometry    : angle       0.54718 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8350 (pt0) cc_final: 0.8114 (pt0)
REVERT: B  376 THR cc_start: 0.8742 (m) cc_final: 0.8126 (p)
REVERT: B  420 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8291 (t0)
REVERT: D   96 ASP cc_start: 0.8209 (p0) cc_final: 0.7333 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1854
  time to fit residues: 27.2148
Evaluate side-chains
  107 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3275 r_free = 0.3275 target = 0.079284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.065442 restraints weight = 16867.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.067950 restraints weight = 8047.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.069606 restraints weight = 5138.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6756  Z= 0.220
  Angle     :  0.590   8.696   9212  Z= 0.312
  Chirality :  0.044   0.144   1000
  Planarity :  0.004   0.050   1184
  Dihedral  :  4.503  16.157    932
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.93 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.28), residues: 842
  helix: -3.89 (0.47), residues: 54
  sheet: -0.16 (0.33), residues: 266
  loop : -1.12 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.002   0.000   HIS A 505 
 PHE   0.048   0.002   PHE B 374 
 TYR   0.010   0.001   TYR D  49 
 ARG   0.003   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02890 (  186)
  hydrogen bonds       : angle       6.19792 (  459)
  SS BOND              : bond        0.00498 (   14)
  SS BOND              : angle       1.22336 (   28)
  covalent geometry    : bond        0.00503 ( 6742)
  covalent geometry    : angle       0.58701 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8325 (pt0) cc_final: 0.8095 (pt0)
REVERT: B  376 THR cc_start: 0.8880 (m) cc_final: 0.8375 (p)
REVERT: B  420 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8269 (t0)
REVERT: D   96 ASP cc_start: 0.8219 (p0) cc_final: 0.7350 (p0)
  outliers start: 15
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1739
  time to fit residues: 23.5071
Evaluate side-chains
  104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 70 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3301 r_free = 0.3301 target = 0.080610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.066669 restraints weight = 16894.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.069226 restraints weight = 8049.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.070862 restraints weight = 5129.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6756  Z= 0.144
  Angle     :  0.549   8.275   9212  Z= 0.290
  Chirality :  0.042   0.141   1000
  Planarity :  0.004   0.042   1184
  Dihedral  :  4.289  15.998    932
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.77 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.28), residues: 842
  helix: -3.84 (0.48), residues: 54
  sheet: -0.13 (0.32), residues: 266
  loop : -1.08 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.010   0.001   PHE B 486 
 TYR   0.009   0.001   TYR D  49 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02595 (  186)
  hydrogen bonds       : angle       6.01837 (  459)
  SS BOND              : bond        0.00407 (   14)
  SS BOND              : angle       1.01381 (   28)
  covalent geometry    : bond        0.00326 ( 6742)
  covalent geometry    : angle       0.54650 ( 9184)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8317 (pt0) cc_final: 0.8084 (pt0)
REVERT: B  376 THR cc_start: 0.8775 (m) cc_final: 0.8403 (p)
REVERT: B  420 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8285 (t0)
REVERT: D   96 ASP cc_start: 0.8180 (p0) cc_final: 0.7310 (p0)
  outliers start: 13
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1759
  time to fit residues: 24.4559
Evaluate side-chains
  108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   58 ASN
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain G residue   79 VAL
Chi-restraints excluded: chain G residue  117 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** 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 = 0.3306 r_free = 0.3306 target = 0.081224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.066963 restraints weight = 17038.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.069564 restraints weight = 8118.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.071248 restraints weight = 5151.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6756  Z= 0.154
  Angle     :  0.558   7.676   9212  Z= 0.295
  Chirality :  0.043   0.146   1000
  Planarity :  0.004   0.040   1184
  Dihedral  :  4.293  19.761    932
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.77 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.28), residues: 842
  helix: -3.87 (0.48), residues: 54
  sheet: -0.16 (0.32), residues: 266
  loop : -1.08 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A 505 
 PHE   0.044   0.001   PHE B 374 
 TYR   0.018   0.001   TYR A 365 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02597 (  186)
  hydrogen bonds       : angle       5.99795 (  459)
  SS BOND              : bond        0.00426 (   14)
  SS BOND              : angle       1.06868 (   28)
  covalent geometry    : bond        0.00352 ( 6742)
  covalent geometry    : angle       0.55546 ( 9184)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2549.03 seconds
wall clock time: 45 minutes 30.01 seconds (2730.01 seconds total)