Starting phenix.real_space_refine
on Thu Mar  6 06:39:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9co9_45774/03_2025/9co9_45774.cif"
  }
  resolution = 3.44
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      26      5.16       5
     C    3305      2.51       5
     N     882      2.21       5
     O     985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5198
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1608
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
    Chain: "A"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1634
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 14, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 978
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
    Chain: "E"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 978
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
  Time building chain proxies: 5.19, per 1000 atoms: 1.00
  Number of scatterers: 5198
  At special positions: 0
  Unit cell: (82.336, 109.781, 118.635, 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      26     16.00
     O     985      8.00
     N     882      7.00
     C    3305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 521 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  50 " - pdb=" SG  CYS D 104 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  50 " - pdb=" SG  CYS E 104 " 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: 1.17
  Conformation dependent library (CDL) restraints added in 607.6 milliseconds
  

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      10.4% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'B' and resid 334 through 340
      removed outlier: 3.765A  pdb=" N   VAL B 338 " --> pdb=" O   PRO B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 407
      removed outlier: 3.759A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 401 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   SER B 405 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 498 through 502
      removed outlier: 3.551A  pdb=" N   GLN B 502 " --> pdb=" O   VAL B 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 380 through 384
      removed outlier: 3.879A  pdb=" N   LEU A 384 " --> pdb=" O   PRO A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 407
      removed outlier: 3.587A  pdb=" N   VAL A 404 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 419
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.600A  pdb=" N   ASP D  90 " --> pdb=" O   LYS D  87 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR D  91 " --> pdb=" O   LEU D  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 91'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.986A  pdb=" N   THR E  91 " --> pdb=" O   LEU E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 351 through 355
      removed outlier: 3.979A  pdb=" N   ASN B 351 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL B 392 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY B 428 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR B 377 " --> pdb=" O   GLY B 428 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL B 430 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AA3, first strand: chain 'B' and resid 470 through 471
      removed outlier: 3.514A  pdb=" N   TYR B 470 " --> pdb=" O   TYR B 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.537A  pdb=" N   ASN A 351 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A 355 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ASN A 391 " --> pdb=" O   GLU A 512 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   GLU A 512 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.504A  pdb=" N   VAL D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASP D  73 " --> pdb=" O   THR D  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12
      removed outlier: 4.167A  pdb=" N   GLY D  10 " --> pdb=" O   GLN D 124 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR D 126 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL D  12 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL D  93 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   THR D  34 " --> pdb=" O   CYS D  50 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   CYS D  50 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.633A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 126 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR E  34 " --> pdb=" O   CYS E  50 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   CYS E  50 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    131 hydrogen bonds defined for protein.
    315 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: 1.26

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1668
        1.35 -     1.47: 1458
        1.47 -     1.60: 2192
        1.60 -     1.73: 0
        1.73 -     1.85: 28
  Bond restraints: 5346
  Sorted by residual:
  bond pdb=" C   PHE B 326 "
       pdb=" N   PRO B 327 "
    ideal  model  delta    sigma   weight residual
    1.331  1.374 -0.043 1.28e-02 6.10e+03 1.12e+01
  bond pdb=" N   GLY A 473 "
       pdb=" CA  GLY A 473 "
    ideal  model  delta    sigma   weight residual
    1.445  1.475 -0.031 9.90e-03 1.02e+04 9.66e+00
  bond pdb=" N   TYR D 110 "
       pdb=" CA  TYR D 110 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.36e-02 5.41e+03 8.63e+00
  bond pdb=" N   GLN A 489 "
       pdb=" CA  GLN A 489 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.18e-02 7.18e+03 8.43e+00
  bond pdb=" N   HIS D  32 "
       pdb=" CA  HIS D  32 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.034 1.18e-02 7.18e+03 8.15e+00
  ... (remaining 5341 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 6948
        2.33 -     4.66: 259
        4.66 -     6.99: 42
        6.99 -     9.32: 12
        9.32 -    11.65: 2
  Bond angle restraints: 7263
  Sorted by residual:
  angle pdb=" N   HIS D  30 "
        pdb=" CA  HIS D  30 "
        pdb=" C   HIS D  30 "
      ideal   model   delta    sigma   weight residual
     114.64  102.99   11.65 1.52e+00 4.33e-01 5.88e+01
  angle pdb=" CA  PHE A 339 "
        pdb=" CB  PHE A 339 "
        pdb=" CG  PHE A 339 "
      ideal   model   delta    sigma   weight residual
     113.80  120.08   -6.28 1.00e+00 1.00e+00 3.95e+01
  angle pdb=" CA  TYR D 110 "
        pdb=" CB  TYR D 110 "
        pdb=" CG  TYR D 110 "
      ideal   model   delta    sigma   weight residual
     113.90  123.49   -9.59 1.80e+00 3.09e-01 2.84e+01
  angle pdb=" N   THR D  31 "
        pdb=" CA  THR D  31 "
        pdb=" C   THR D  31 "
      ideal   model   delta    sigma   weight residual
     114.12  107.44    6.68 1.39e+00 5.18e-01 2.31e+01
  angle pdb=" O   TYR D 109 "
        pdb=" C   TYR D 109 "
        pdb=" N   TYR D 110 "
      ideal   model   delta    sigma   weight residual
     123.27  117.86    5.41 1.16e+00 7.43e-01 2.18e+01
  ... (remaining 7258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 2839
       17.97 -    35.93: 251
       35.93 -    53.90: 35
       53.90 -    71.86: 8
       71.86 -    89.82: 2
  Dihedral angle restraints: 3135
    sinusoidal: 1222
      harmonic: 1913
  Sorted by residual:
  dihedral pdb=" CB  CYS B 477 "
           pdb=" SG  CYS B 477 "
           pdb=" SG  CYS B 484 "
           pdb=" CB  CYS B 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -16.00  -70.00     1      1.00e+01 1.00e-02 6.32e+01
  dihedral pdb=" CB  CYS A 388 "
           pdb=" SG  CYS A 388 "
           pdb=" SG  CYS A 521 "
           pdb=" CB  CYS A 521 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.69   54.31     1      1.00e+01 1.00e-02 4.00e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.44  -47.44     1      1.00e+01 1.00e-02 3.11e+01
  ... (remaining 3132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 502
       0.053 -    0.106: 188
       0.106 -    0.159: 49
       0.159 -    0.213: 12
       0.213 -    0.266: 2
  Chirality restraints: 753
  Sorted by residual:
  chirality pdb=" CA  PRO A 495 "
            pdb=" N   PRO A 495 "
            pdb=" C   PRO A 495 "
            pdb=" CB  PRO A 495 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  ILE A 465 "
            pdb=" N   ILE A 465 "
            pdb=" C   ILE A 465 "
            pdb=" CB  ILE A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASN A 391 "
            pdb=" N   ASN A 391 "
            pdb=" C   ASN A 391 "
            pdb=" CB  ASN A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 750 not shown)

  Planarity restraints: 950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 109 "    0.021 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   TYR D 109 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   TYR D 109 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR D 110 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 494 "   -0.315 9.50e-02 1.11e+02   1.41e-01 1.22e+01
        pdb=" NE  ARG A 494 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 494 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 494 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 494 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  28 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.16e+00
        pdb=" C   ALA D  28 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ALA D  28 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU D  29 "    0.015 2.00e-02 2.50e+03
  ... (remaining 947 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1747
        2.84 -     3.36: 4242
        3.36 -     3.87: 8070
        3.87 -     4.39: 9034
        4.39 -     4.90: 15888
  Nonbonded interactions: 38981
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 114 "
            pdb=" N   PHE D 116 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   LEU D  29 "
            pdb=" NH1 ARG D  72 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OG1 THR B 412 "
            pdb=" OD2 ASP B 417 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   SER B 510 "
            pdb=" OG  SER B 510 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" OD2 ASP A 395 "
            pdb=" OH  TYR A 420 "
     model   vdw
     2.405 3.040
  ... (remaining 38976 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 326 through 525)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             17.150
  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:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.970
  Find NCS groups from input model:        0.180
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
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      :  0.006   0.049   5346  Z= 0.378
  Angle     :  1.021  11.654   7263  Z= 0.610
  Chirality :  0.059   0.266    753
  Planarity :  0.008   0.141    950
  Dihedral  : 12.974  89.824   1893
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.28 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  1.43 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.30), residues: 653
  helix: -4.28 (0.37), residues: 51
  sheet:  0.13 (0.45), residues: 147
  loop : -1.96 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 449 
 HIS   0.007   0.001   HIS A 336 
 PHE   0.032   0.002   PHE A 335 
 TYR   0.031   0.002   TYR D 110 
 ARG   0.014   0.001   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 209
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   80 TYR cc_start: 0.7805 (m-80) cc_final: 0.6855 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 211
  average time/residue: 0.2648
  time to fit residues: 68.3851
Evaluate side-chains
  132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0370
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
B 489 GLN
A 489 GLN
D  82 GLN
D 121 GLN
E  13 GLN
E  32 HIS
E  74 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.109999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.085078 restraints weight = 14005.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 4.25
r_work: 0.3175 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5346  Z= 0.239
  Angle     :  0.749   9.043   7263  Z= 0.383
  Chirality :  0.048   0.175    753
  Planarity :  0.005   0.047    950
  Dihedral  :  5.341  25.826    738
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.51 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.28 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.31), residues: 653
  helix: -3.83 (0.46), residues: 55
  sheet:  0.39 (0.42), residues: 172
  loop : -1.70 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 449 
 HIS   0.003   0.001   HIS B 515 
 PHE   0.021   0.001   PHE E  68 
 TYR   0.024   0.002   TYR D 110 
 ARG   0.009   0.001   ARG D  38 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8475 (tpp80)
REVERT: B  411 GLN cc_start: 0.7372 (mp10) cc_final: 0.7105 (mp10)
REVERT: B  462 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7348 (tm-30)
REVERT: A  403 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8682 (mt-10)
REVERT: A  464 ASP cc_start: 0.8416 (t0) cc_final: 0.8122 (t70)
REVERT: A  496 THR cc_start: 0.8850 (p) cc_final: 0.8566 (p)
REVERT: A  514 LEU cc_start: 0.7196 (tt) cc_final: 0.6589 (tt)
REVERT: D   36 TRP cc_start: 0.8091 (m100) cc_final: 0.7824 (m100)
REVERT: D   44 GLU cc_start: 0.8214 (tp30) cc_final: 0.7505 (tp30)
REVERT: D   59 TYR cc_start: 0.8859 (m-80) cc_final: 0.8213 (m-80)
REVERT: D   77 ASN cc_start: 0.8863 (t0) cc_final: 0.7867 (t0)
REVERT: D   95 TYR cc_start: 0.7319 (m-80) cc_final: 0.7091 (m-80)
REVERT: D  115 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7996 (p0)
REVERT: D  125 VAL cc_start: 0.9248 (t) cc_final: 0.8965 (p)
REVERT: E   13 GLN cc_start: 0.8408 (mm110) cc_final: 0.8168 (mm-40)
REVERT: E   19 ARG cc_start: 0.9048 (ttt-90) cc_final: 0.8700 (ttt-90)
REVERT: E   68 PHE cc_start: 0.7856 (m-10) cc_final: 0.7652 (m-80)
REVERT: E   87 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8202 (ttpt)
REVERT: E   89 GLU cc_start: 0.9167 (pm20) cc_final: 0.8029 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 152
  average time/residue: 0.1862
  time to fit residues: 35.8777
Evaluate side-chains
  136 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  358 CYS
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  115 ASP
Chi-restraints excluded: chain E residue   74 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.108114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.082227 restraints weight = 13949.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 4.36
r_work: 0.3142 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5346  Z= 0.232
  Angle     :  0.681   8.407   7263  Z= 0.348
  Chirality :  0.046   0.169    753
  Planarity :  0.005   0.046    950
  Dihedral  :  5.027  22.695    736
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.67 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.53 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.31), residues: 653
  helix: -3.50 (0.54), residues: 47
  sheet:  0.41 (0.40), residues: 182
  loop : -1.73 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 433 
 HIS   0.004   0.001   HIS D  32 
 PHE   0.013   0.001   PHE E  68 
 TYR   0.032   0.001   TYR D  94 
 ARG   0.004   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  343 ARG cc_start: 0.8830 (ptp90) cc_final: 0.8594 (ptp90)
REVERT: A  403 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8785 (mt-10)
REVERT: A  464 ASP cc_start: 0.8399 (t0) cc_final: 0.8165 (t70)
REVERT: A  496 THR cc_start: 0.8921 (p) cc_final: 0.8648 (p)
REVERT: D   19 ARG cc_start: 0.9201 (ttm-80) cc_final: 0.8883 (ttt90)
REVERT: D   38 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.8017 (mmm-85)
REVERT: D   44 GLU cc_start: 0.8332 (tp30) cc_final: 0.7765 (tp30)
REVERT: D   59 TYR cc_start: 0.8878 (m-80) cc_final: 0.8319 (m-80)
REVERT: D   77 ASN cc_start: 0.8767 (t0) cc_final: 0.7834 (t0)
REVERT: D  113 ASP cc_start: 0.8512 (m-30) cc_final: 0.7863 (t0)
REVERT: D  125 VAL cc_start: 0.9071 (t) cc_final: 0.8855 (m)
REVERT: E    3 GLN cc_start: 0.8778 (mm110) cc_final: 0.7506 (mm-40)
  outliers start: 17
  outliers final: 13
  residues processed: 144
  average time/residue: 0.1916
  time to fit residues: 35.1553
Evaluate side-chains
  131 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  358 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   74 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 50 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 41 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.108726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.082524 restraints weight = 14326.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 4.47
r_work: 0.3147 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5346  Z= 0.194
  Angle     :  0.665   8.895   7263  Z= 0.338
  Chirality :  0.045   0.149    753
  Planarity :  0.004   0.038    950
  Dihedral  :  4.773  20.681    736
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.05 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.60 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.32), residues: 653
  helix: -3.27 (0.58), residues: 47
  sheet:  0.57 (0.40), residues: 183
  loop : -1.64 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.004   0.001   HIS D  32 
 PHE   0.023   0.001   PHE E  68 
 TYR   0.013   0.001   TYR D  94 
 ARG   0.003   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8374 (ttp80)
REVERT: B  395 ASP cc_start: 0.9069 (p0) cc_final: 0.8411 (p0)
REVERT: B  462 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7453 (tm-30)
REVERT: A  403 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8789 (mt-10)
REVERT: A  464 ASP cc_start: 0.8424 (t0) cc_final: 0.8101 (t0)
REVERT: A  496 THR cc_start: 0.8891 (p) cc_final: 0.8610 (p)
REVERT: D    4 LEU cc_start: 0.8981 (mt) cc_final: 0.8562 (pp)
REVERT: D   19 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.8978 (ttt90)
REVERT: D   44 GLU cc_start: 0.8311 (tp30) cc_final: 0.7919 (tp30)
REVERT: D   59 TYR cc_start: 0.8903 (m-80) cc_final: 0.8301 (m-80)
REVERT: D   77 ASN cc_start: 0.8802 (t0) cc_final: 0.7883 (t0)
REVERT: D  113 ASP cc_start: 0.8479 (m-30) cc_final: 0.7735 (t0)
REVERT: E   19 ARG cc_start: 0.9121 (ttt-90) cc_final: 0.8704 (ttt-90)
  outliers start: 20
  outliers final: 13
  residues processed: 140
  average time/residue: 0.1778
  time to fit residues: 31.9798
Evaluate side-chains
  137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  358 CYS
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   74 ASN
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.105629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.080629 restraints weight = 14091.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 4.42
r_work: 0.3067 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   5346  Z= 0.357
  Angle     :  0.730   8.460   7263  Z= 0.379
  Chirality :  0.047   0.198    753
  Planarity :  0.005   0.041    950
  Dihedral  :  5.463  30.044    736
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.58 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 17.53 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.63 (0.32), residues: 653
  helix: -3.35 (0.58), residues: 48
  sheet:  0.54 (0.40), residues: 185
  loop : -1.65 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 433 
 HIS   0.006   0.002   HIS B 515 
 PHE   0.032   0.002   PHE E  68 
 TYR   0.016   0.002   TYR D  94 
 ARG   0.003   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8521 (ttp80)
REVERT: B  368 PHE cc_start: 0.8281 (t80) cc_final: 0.7709 (t80)
REVERT: B  395 ASP cc_start: 0.9056 (p0) cc_final: 0.8595 (p0)
REVERT: A  389 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8344 (p90)
REVERT: A  403 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8887 (mt-10)
REVERT: A  464 ASP cc_start: 0.8474 (t0) cc_final: 0.8150 (t0)
REVERT: D   19 ARG cc_start: 0.9211 (ttm-80) cc_final: 0.8851 (ttt90)
REVERT: D   44 GLU cc_start: 0.8452 (tp30) cc_final: 0.8085 (tp30)
REVERT: D   59 TYR cc_start: 0.8969 (m-80) cc_final: 0.8628 (m-80)
REVERT: D   77 ASN cc_start: 0.9010 (t0) cc_final: 0.8150 (t0)
REVERT: D   82 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8594 (tm-30)
REVERT: D  113 ASP cc_start: 0.8485 (m-30) cc_final: 0.7579 (t0)
REVERT: D  117 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7929 (t80)
REVERT: E   44 GLU cc_start: 0.8957 (mp0) cc_final: 0.8451 (mp0)
REVERT: E   46 GLU cc_start: 0.8127 (pm20) cc_final: 0.7592 (pm20)
  outliers start: 30
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1630
  time to fit residues: 29.5707
Evaluate side-chains
  139 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  439 ASP
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  115 ASP
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0570
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 60 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.107659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.082652 restraints weight = 13886.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.42
r_work: 0.3124 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5346  Z= 0.202
  Angle     :  0.686   8.663   7263  Z= 0.349
  Chirality :  0.045   0.156    753
  Planarity :  0.004   0.042    950
  Dihedral  :  4.825  21.159    736
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.90 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.00 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.32), residues: 653
  helix: -3.37 (0.52), residues: 55
  sheet:  0.68 (0.41), residues: 175
  loop : -1.46 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 449 
 HIS   0.004   0.001   HIS D  32 
 PHE   0.009   0.001   PHE D  37 
 TYR   0.011   0.001   TYR D 111 
 ARG   0.002   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8153 (t80) cc_final: 0.7708 (t80)
REVERT: B  395 ASP cc_start: 0.9059 (p0) cc_final: 0.8546 (p0)
REVERT: B  462 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: A  403 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8864 (mt-10)
REVERT: A  464 ASP cc_start: 0.8389 (t0) cc_final: 0.8077 (t0)
REVERT: D    3 GLN cc_start: 0.8427 (pm20) cc_final: 0.8181 (pm20)
REVERT: D    4 LEU cc_start: 0.8996 (mt) cc_final: 0.8699 (pp)
REVERT: D   44 GLU cc_start: 0.8458 (tp30) cc_final: 0.8073 (tp30)
REVERT: D   59 TYR cc_start: 0.9063 (m-80) cc_final: 0.8502 (m-80)
REVERT: D   67 ARG cc_start: 0.9074 (mtm-85) cc_final: 0.8569 (mtm-85)
REVERT: D   77 ASN cc_start: 0.8981 (t0) cc_final: 0.8176 (t0)
REVERT: D   82 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8546 (tm-30)
REVERT: D  113 ASP cc_start: 0.8470 (m-30) cc_final: 0.7310 (t0)
REVERT: D  115 ASP cc_start: 0.8364 (m-30) cc_final: 0.7522 (p0)
REVERT: D  117 TYR cc_start: 0.8758 (t80) cc_final: 0.7847 (t80)
REVERT: D  121 GLN cc_start: 0.8820 (mp10) cc_final: 0.8359 (pm20)
REVERT: E   44 GLU cc_start: 0.8873 (mp0) cc_final: 0.8300 (mp0)
REVERT: E   46 GLU cc_start: 0.8003 (pm20) cc_final: 0.7494 (pm20)
REVERT: E   73 ASP cc_start: 0.9194 (t0) cc_final: 0.8992 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1668
  time to fit residues: 30.2162
Evaluate side-chains
  137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.0156

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 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 = 0.3696 r_free = 0.3696 target = 0.105854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.080657 restraints weight = 13861.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 4.41
r_work: 0.3078 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5346  Z= 0.300
  Angle     :  0.717   8.416   7263  Z= 0.366
  Chirality :  0.046   0.171    753
  Planarity :  0.004   0.044    950
  Dihedral  :  5.057  23.780    736
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.82 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.00 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.32), residues: 653
  helix: -3.27 (0.59), residues: 49
  sheet:  0.71 (0.41), residues: 174
  loop : -1.62 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.006   0.001   HIS B 515 
 PHE   0.009   0.001   PHE D  37 
 TYR   0.012   0.001   TYR B 377 
 ARG   0.006   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8378 (ttp80)
REVERT: B  368 PHE cc_start: 0.8354 (t80) cc_final: 0.7775 (t80)
REVERT: B  395 ASP cc_start: 0.8973 (p0) cc_final: 0.8554 (p0)
REVERT: A  389 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8332 (p90)
REVERT: A  403 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8893 (mt-10)
REVERT: A  464 ASP cc_start: 0.8403 (t0) cc_final: 0.7882 (t0)
REVERT: D   44 GLU cc_start: 0.8629 (tp30) cc_final: 0.8381 (tp30)
REVERT: D   59 TYR cc_start: 0.8999 (m-80) cc_final: 0.8540 (m-80)
REVERT: D   67 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8826 (mtm-85)
REVERT: D   77 ASN cc_start: 0.9128 (t0) cc_final: 0.8448 (t0)
REVERT: D   82 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8576 (tm-30)
REVERT: D   95 TYR cc_start: 0.7250 (m-80) cc_final: 0.6973 (m-80)
REVERT: D  117 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7868 (t80)
REVERT: D  121 GLN cc_start: 0.8648 (mp10) cc_final: 0.8198 (pm20)
REVERT: E   44 GLU cc_start: 0.8975 (mp0) cc_final: 0.8448 (mp0)
REVERT: E   46 GLU cc_start: 0.8172 (pm20) cc_final: 0.7646 (pm20)
  outliers start: 19
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1747
  time to fit residues: 29.6039
Evaluate side-chains
  136 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  439 ASP
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   76 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 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 = 0.3696 r_free = 0.3696 target = 0.106037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.080868 restraints weight = 13958.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 4.41
r_work: 0.3087 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5346  Z= 0.267
  Angle     :  0.735  11.508   7263  Z= 0.372
  Chirality :  0.047   0.236    753
  Planarity :  0.004   0.044    950
  Dihedral  :  5.006  23.007    736
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.36 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.08 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.32), residues: 653
  helix: -3.29 (0.53), residues: 55
  sheet:  0.70 (0.41), residues: 174
  loop : -1.61 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.005   0.001   HIS B 515 
 PHE   0.009   0.001   PHE D  37 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.003   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8285 (t80) cc_final: 0.7670 (t80)
REVERT: B  395 ASP cc_start: 0.8979 (p0) cc_final: 0.8617 (p0)
REVERT: B  462 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: A  389 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8391 (p90)
REVERT: A  403 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8893 (mt-10)
REVERT: A  464 ASP cc_start: 0.8426 (t0) cc_final: 0.7931 (t0)
REVERT: D    4 LEU cc_start: 0.9111 (mt) cc_final: 0.8674 (pp)
REVERT: D   59 TYR cc_start: 0.9100 (m-80) cc_final: 0.8700 (m-80)
REVERT: D   64 VAL cc_start: 0.9307 (m) cc_final: 0.9101 (m)
REVERT: D   67 ARG cc_start: 0.9129 (mtm-85) cc_final: 0.8625 (mtm-85)
REVERT: D   77 ASN cc_start: 0.9124 (t0) cc_final: 0.8497 (t0)
REVERT: D   82 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8565 (tm-30)
REVERT: D  110 TYR cc_start: 0.8495 (t80) cc_final: 0.8248 (t80)
REVERT: D  117 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7951 (t80)
REVERT: D  121 GLN cc_start: 0.8715 (mp10) cc_final: 0.8264 (pm20)
REVERT: E   44 GLU cc_start: 0.8947 (mp0) cc_final: 0.8410 (mp0)
REVERT: E   46 GLU cc_start: 0.8260 (pm20) cc_final: 0.7724 (pm20)
  outliers start: 21
  outliers final: 14
  residues processed: 130
  average time/residue: 0.1743
  time to fit residues: 29.4097
Evaluate side-chains
  130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 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 = 0.3690 r_free = 0.3690 target = 0.105387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.081041 restraints weight = 14315.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 4.41
r_work: 0.3070 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.5590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5346  Z= 0.304
  Angle     :  0.767  11.906   7263  Z= 0.388
  Chirality :  0.047   0.197    753
  Planarity :  0.004   0.044    950
  Dihedral  :  5.173  24.039    736
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.97 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.61 %
    Favored  : 72.63 %
  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: -1.57 (0.32), residues: 653
  helix: -3.12 (0.60), residues: 49
  sheet:  0.59 (0.40), residues: 181
  loop : -1.62 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.005   0.001   HIS B 515 
 PHE   0.013   0.001   PHE B 397 
 TYR   0.021   0.001   TYR D  95 
 ARG   0.005   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8358 (t80) cc_final: 0.7669 (t80)
REVERT: B  395 ASP cc_start: 0.8964 (p0) cc_final: 0.8614 (p0)
REVERT: B  462 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: A  389 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8336 (p90)
REVERT: A  403 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8908 (mt-10)
REVERT: A  464 ASP cc_start: 0.8434 (t0) cc_final: 0.7900 (t0)
REVERT: D   44 GLU cc_start: 0.8357 (tp30) cc_final: 0.8115 (tp30)
REVERT: D   59 TYR cc_start: 0.9033 (m-80) cc_final: 0.8616 (m-80)
REVERT: D   67 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8610 (mtm-85)
REVERT: D   77 ASN cc_start: 0.9144 (t0) cc_final: 0.8556 (t0)
REVERT: D   80 TYR cc_start: 0.8545 (m-80) cc_final: 0.8321 (m-80)
REVERT: D   82 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8551 (tm-30)
REVERT: D   83 MET cc_start: 0.8751 (mmm) cc_final: 0.8456 (mmm)
REVERT: D  118 TYR cc_start: 0.9050 (m-10) cc_final: 0.8704 (m-10)
REVERT: D  121 GLN cc_start: 0.8651 (mp10) cc_final: 0.8205 (pm20)
REVERT: E   44 GLU cc_start: 0.8983 (mp0) cc_final: 0.8386 (mp0)
REVERT: E   46 GLU cc_start: 0.8277 (pm20) cc_final: 0.7715 (pm20)
REVERT: E   76 LYS cc_start: 0.9434 (mtmm) cc_final: 0.9210 (mtmm)
  outliers start: 21
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1784
  time to fit residues: 29.5528
Evaluate side-chains
  130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  439 ASP
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 21 optimal weight:    0.3980
   chunk 5 optimal weight:    0.1980
   chunk 50 optimal weight:    0.2980
   chunk 47 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 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 = 0.3729 r_free = 0.3729 target = 0.107905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.081679 restraints weight = 14091.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 4.38
r_work: 0.3125 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.5650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5346  Z= 0.222
  Angle     :  0.740  10.433   7263  Z= 0.373
  Chirality :  0.047   0.215    753
  Planarity :  0.004   0.045    950
  Dihedral  :  4.782  20.233    736
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.82 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 25.22 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.32), residues: 653
  helix: -2.91 (0.59), residues: 55
  sheet:  0.63 (0.41), residues: 174
  loop : -1.47 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 433 
 HIS   0.004   0.001   HIS D  32 
 PHE   0.009   0.001   PHE D  37 
 TYR   0.009   0.001   TYR B 491 
 ARG   0.006   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.9000 (tmm-80) cc_final: 0.8594 (ttp80)
REVERT: B  368 PHE cc_start: 0.8310 (t80) cc_final: 0.7788 (t80)
REVERT: B  462 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7562 (tm-30)
REVERT: A  403 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8888 (mt-10)
REVERT: A  464 ASP cc_start: 0.8378 (t0) cc_final: 0.7883 (t0)
REVERT: D   44 GLU cc_start: 0.8346 (tp30) cc_final: 0.8052 (tp30)
REVERT: D   59 TYR cc_start: 0.9100 (m-80) cc_final: 0.8511 (m-80)
REVERT: D   77 ASN cc_start: 0.9108 (t0) cc_final: 0.8597 (t0)
REVERT: D   80 TYR cc_start: 0.8490 (m-80) cc_final: 0.8215 (m-80)
REVERT: D   82 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8581 (tm-30)
REVERT: D  118 TYR cc_start: 0.9046 (m-10) cc_final: 0.8759 (m-10)
REVERT: D  121 GLN cc_start: 0.8658 (mp10) cc_final: 0.8279 (pm20)
REVERT: E   44 GLU cc_start: 0.8917 (mp0) cc_final: 0.8319 (mp0)
REVERT: E   46 GLU cc_start: 0.8183 (pm20) cc_final: 0.7658 (pm20)
  outliers start: 14
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1684
  time to fit residues: 27.3420
Evaluate side-chains
  126 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 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 = 0.3706 r_free = 0.3706 target = 0.106483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.081280 restraints weight = 14139.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 4.37
r_work: 0.3096 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.5706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5346  Z= 0.270
  Angle     :  0.753  10.688   7263  Z= 0.381
  Chirality :  0.047   0.205    753
  Planarity :  0.004   0.044    950
  Dihedral  :  4.956  21.750    736
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.97 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 25.04 %
    Favored  : 72.63 %
  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: -1.52 (0.32), residues: 653
  helix: -2.89 (0.59), residues: 55
  sheet:  0.60 (0.41), residues: 178
  loop : -1.56 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.005   0.001   HIS B 515 
 PHE   0.010   0.001   PHE B 397 
 TYR   0.011   0.001   TYR D  94 
 ARG   0.008   0.001   ARG D  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3927.45 seconds
wall clock time: 69 minutes 14.80 seconds (4154.80 seconds total)