Starting phenix.real_space_refine
on Fri Feb 14 14:01:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4d_30076/02_2025/6m4d_30076.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     P     250      5.49       5
     S      14      5.16       5
     C    5801      2.51       5
     N    1962      2.21       5
     O    2470      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10497
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 693
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "D"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2548
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2577
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
  Restraints were copied for chains:
    E, F, G, H
  Time building chain proxies: 6.20, per 1000 atoms: 0.59
  Number of scatterers: 10497
  At special positions: 0
  Unit cell: (131.04, 79.04, 114.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     250     15.00
     O    2470      8.00
     N    1962      7.00
     C    5801      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 683.3 milliseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1272

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      75.1% alpha, 0.9% beta
      123 base pairs and 185 stacking pairs defined.
    Time for finding SS restraints: 4.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.724A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 18 through 24
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 47 through 75
    Processing helix  chain 'C' and resid 82 through 91
      removed outlier: 3.571A  pdb=" N   LEU C  86 " --> pdb=" O   THR C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 100
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 63 through 77
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.723A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 50 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 18 through 24
    Processing helix  chain 'G' and resid 28 through 38
    Processing helix  chain 'G' and resid 47 through 75
    Processing helix  chain 'G' and resid 82 through 91
      removed outlier: 3.571A  pdb=" N   LEU G  86 " --> pdb=" O   THR G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 100
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.952A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.068A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    381 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      317 hydrogen bonds
      622 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      185 stacking parallelities
  Total time for adding SS restraints: 3.20

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1934
        1.33 -     1.45: 3674
        1.45 -     1.57: 5056
        1.57 -     1.68: 498
        1.68 -     1.80: 24
  Bond restraints: 11186
  Sorted by residual:
  bond pdb=" P    DG J 136 "
       pdb=" O5'  DG J 136 "
    ideal  model  delta    sigma   weight residual
    1.600  1.639 -0.039 2.00e-02 2.50e+03 3.89e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.473 -0.051 3.00e-02 1.11e+03 2.85e+00
  bond pdb=" C5'  DG J 136 "
       pdb=" C4'  DG J 136 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 2.00e-02 2.50e+03 2.66e+00
  bond pdb=" C1'  DC I  56 "
       pdb=" N1   DC I  56 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.62e+00
  bond pdb=" C3'  DT J 128 "
       pdb=" O3'  DT J 128 "
    ideal  model  delta    sigma   weight residual
    1.422  1.470 -0.048 3.00e-02 1.11e+03 2.59e+00
  ... (remaining 11181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 15964
        2.78 -     5.56: 196
        5.56 -     8.35: 7
        8.35 -    11.13: 5
       11.13 -    13.91: 1
  Bond angle restraints: 16173
  Sorted by residual:
  angle pdb=" O3'  DC J 135 "
        pdb=" P    DG J 136 "
        pdb=" O5'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     104.00  117.91  -13.91 1.50e+00 4.44e-01 8.60e+01
  angle pdb=" C3'  DC J 135 "
        pdb=" O3'  DC J 135 "
        pdb=" P    DG J 136 "
      ideal   model   delta    sigma   weight residual
     120.20  131.11  -10.91 1.50e+00 4.44e-01 5.29e+01
  angle pdb=" P    DG J 136 "
        pdb=" O5'  DG J 136 "
        pdb=" C5'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     120.00  125.98   -5.98 1.50e+00 4.44e-01 1.59e+01
  angle pdb=" C3'  DC I 111 "
        pdb=" C2'  DC I 111 "
        pdb=" C1'  DC I 111 "
      ideal   model   delta    sigma   weight residual
     101.60   96.35    5.25 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" C5'  DG J 136 "
        pdb=" C4'  DG J 136 "
        pdb=" O4'  DG J 136 "
      ideal   model   delta    sigma   weight residual
     109.40  114.50   -5.10 1.50e+00 4.44e-01 1.16e+01
  ... (remaining 16168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 4628
       34.98 -    69.96: 1358
       69.96 -   104.94: 65
      104.94 -   139.92: 7
      139.92 -   174.90: 2
  Dihedral angle restraints: 6060
    sinusoidal: 4090
      harmonic: 1970
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.08   22.92     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  LYS D  34 "
           pdb=" C   LYS D  34 "
           pdb=" N   GLU D  35 "
           pdb=" CA  GLU D  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.78  -22.22     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 6057 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1609
       0.069 -    0.138: 218
       0.138 -    0.207: 19
       0.207 -    0.276: 3
       0.276 -    0.345: 1
  Chirality restraints: 1850
  Sorted by residual:
  chirality pdb=" C1'  DT J  13 "
            pdb=" O4'  DT J  13 "
            pdb=" C2'  DT J  13 "
            pdb=" N1   DT J  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.12    0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" C1'  DG I  19 "
            pdb=" O4'  DG I  19 "
            pdb=" C2'  DG I  19 "
            pdb=" N9   DG I  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.17    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" P    DG J 136 "
            pdb=" OP1  DG J 136 "
            pdb=" OP2  DG J 136 "
            pdb=" O5'  DG J 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.59   -0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 1847 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  13 "   -0.036 2.00e-02 2.50e+03   2.52e-02 1.91e+01
        pdb=" N9   DG I  13 "    0.069 2.00e-02 2.50e+03
        pdb=" C8   DG I  13 "   -0.030 2.00e-02 2.50e+03
        pdb=" N7   DG I  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  13 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  13 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DG I  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  13 "    0.016 2.00e-02 2.50e+03
        pdb=" N2   DG I  13 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DG I  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DG I  13 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  14 "    0.026 2.00e-02 2.50e+03   2.54e-02 1.78e+01
        pdb=" N9   DA J  14 "   -0.068 2.00e-02 2.50e+03
        pdb=" C8   DA J  14 "    0.040 2.00e-02 2.50e+03
        pdb=" N7   DA J  14 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA J  14 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6   DA J  14 "   -0.000 2.00e-02 2.50e+03
        pdb=" N6   DA J  14 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1   DA J  14 "    0.015 2.00e-02 2.50e+03
        pdb=" C2   DA J  14 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA J  14 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DA J  14 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C  72 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ALA C  72 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA C  72 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER C  73 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 352
        2.64 -     3.20: 10613
        3.20 -     3.77: 22149
        3.77 -     4.33: 26096
        4.33 -     4.90: 35636
  Nonbonded interactions: 94846
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OP2  DC I  82 "
     model   vdw
     2.074 3.120
  nonbonded pdb=" OG  SER C  73 "
            pdb=" O   VAL C  78 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OG  SER G  73 "
            pdb=" O   VAL G  78 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" N2   DG I 132 "
            pdb=" O2   DC J  16 "
     model   vdw
     2.099 2.496
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH1 ARG H  92 "
     model   vdw
     2.154 3.120
  ... (remaining 94841 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'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             0.690
  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:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.680
  Find NCS groups from input model:        0.190
  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:2.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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      :  0.007   0.051  11186  Z= 0.384
  Angle     :  0.836  13.910  16173  Z= 0.502
  Chirality :  0.048   0.345   1850
  Planarity :  0.005   0.068   1178
  Dihedral  : 31.368 174.897   4788
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 25.84
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  6.61 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.06 %
    Favored  : 87.23 %
  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: -2.81 (0.26), residues: 666
  helix: -1.35 (0.20), residues: 490
  sheet:  None (None), residues: 0
  loop : -2.95 (0.34), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E 113 
 PHE   0.015   0.003   PHE F 100 
 TYR   0.015   0.002   TYR D  40 
 ARG   0.004   0.001   ARG C  31 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.834 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7993 (mmp-170) cc_final: 0.7259 (mmp80)
REVERT: A   84 PHE cc_start: 0.8620 (m-80) cc_final: 0.8362 (m-80)
REVERT: A   90 MET cc_start: 0.8269 (mtp) cc_final: 0.7949 (mtp)
REVERT: A   93 GLN cc_start: 0.9115 (tt0) cc_final: 0.8566 (tt0)
REVERT: A   97 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8698 (mt-10)
REVERT: A  123 ASP cc_start: 0.8910 (m-30) cc_final: 0.8613 (m-30)
REVERT: B   27 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8814 (tm-30)
REVERT: B   63 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: B   88 TYR cc_start: 0.8335 (m-10) cc_final: 0.8043 (m-80)
REVERT: D   46 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8174 (pttt)
REVERT: D   59 MET cc_start: 0.8768 (tpp) cc_final: 0.8280 (tpt)
REVERT: D   83 TYR cc_start: 0.7935 (m-10) cc_final: 0.7478 (m-10)
REVERT: D  105 GLU cc_start: 0.8753 (pp20) cc_final: 0.7935 (pm20)
REVERT: D  106 LEU cc_start: 0.8870 (mt) cc_final: 0.8608 (mt)
REVERT: E   60 LEU cc_start: 0.8172 (mt) cc_final: 0.7943 (mt)
REVERT: E   97 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8687 (mt-10)
REVERT: E  100 LEU cc_start: 0.9430 (tp) cc_final: 0.9150 (tt)
REVERT: F   88 TYR cc_start: 0.8285 (m-10) cc_final: 0.7234 (m-80)
REVERT: G   36 LEU cc_start: 0.9529 (tt) cc_final: 0.9310 (mm)
REVERT: G   46 VAL cc_start: 0.8463 (t) cc_final: 0.8236 (t)
REVERT: H   59 MET cc_start: 0.8789 (tpp) cc_final: 0.8525 (tpp)
REVERT: H  105 GLU cc_start: 0.8773 (pp20) cc_final: 0.8550 (pp20)
  outliers start: 4
  outliers final: 3
  residues processed: 218
  average time/residue: 0.3279
  time to fit residues: 90.4155
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
C  71 ASN
H  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.048185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.037112 restraints weight = 85897.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.038247 restraints weight = 47867.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.038981 restraints weight = 32721.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11186  Z= 0.217
  Angle     :  0.706   8.339  16173  Z= 0.412
  Chirality :  0.041   0.230   1850
  Planarity :  0.005   0.064   1178
  Dihedral  : 34.558 173.269   3476
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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: -0.13 (0.31), residues: 666
  helix:  0.84 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.11 (0.34), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  82 
 PHE   0.013   0.002   PHE E  67 
 TYR   0.013   0.002   TYR F  98 
 ARG   0.005   0.001   ARG C  45 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.849 
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: symmetry clash
REVERT: A   62 ILE cc_start: 0.9237 (mm) cc_final: 0.8969 (mm)
REVERT: A   63 ARG cc_start: 0.8536 (mmp-170) cc_final: 0.7882 (mmp80)
REVERT: A   84 PHE cc_start: 0.8860 (m-80) cc_final: 0.8472 (m-80)
REVERT: A   93 GLN cc_start: 0.9070 (tt0) cc_final: 0.8651 (tt0)
REVERT: A   97 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8684 (mt-10)
REVERT: A  126 LEU cc_start: 0.9501 (tp) cc_final: 0.9248 (tp)
REVERT: B   27 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8885 (tm-30)
REVERT: B   49 LEU cc_start: 0.9174 (mp) cc_final: 0.8902 (mp)
REVERT: C   31 ARG cc_start: 0.8660 (ttm170) cc_final: 0.7935 (ttp80)
REVERT: D   62 MET cc_start: 0.9213 (tpp) cc_final: 0.8980 (tpp)
REVERT: D   71 GLU cc_start: 0.8535 (tp30) cc_final: 0.8324 (tp30)
REVERT: D   83 TYR cc_start: 0.7955 (m-10) cc_final: 0.7527 (m-80)
REVERT: D  102 LEU cc_start: 0.8479 (tp) cc_final: 0.8271 (tp)
REVERT: D  109 HIS cc_start: 0.8980 (m170) cc_final: 0.8710 (m90)
REVERT: E   93 GLN cc_start: 0.9240 (tt0) cc_final: 0.8697 (tp40)
REVERT: E   97 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8208 (mt-10)
REVERT: E  100 LEU cc_start: 0.9287 (tp) cc_final: 0.8996 (tp)
REVERT: F   27 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8976 (mp10)
REVERT: F   58 LEU cc_start: 0.9239 (tt) cc_final: 0.9014 (pp)
REVERT: F   63 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7970 (mt-10)
REVERT: G   31 ARG cc_start: 0.8667 (ttm170) cc_final: 0.8451 (ttp80)
REVERT: G   36 LEU cc_start: 0.9621 (tt) cc_final: 0.9380 (mm)
REVERT: H   79 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8165 (mtp85)
REVERT: H   83 TYR cc_start: 0.7559 (m-10) cc_final: 0.7056 (m-80)
REVERT: H   95 GLN cc_start: 0.9258 (tt0) cc_final: 0.8984 (tt0)
REVERT: H  102 LEU cc_start: 0.8680 (tp) cc_final: 0.8410 (tp)
REVERT: H  109 HIS cc_start: 0.9121 (m170) cc_final: 0.8739 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2878
  time to fit residues: 77.5940
Evaluate side-chains
  162 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 HIS
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  33 HIS
G  43 HIS
H  63 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.045179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.033582 restraints weight = 91478.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.034616 restraints weight = 53576.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.035313 restraints weight = 37921.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  11186  Z= 0.402
  Angle     :  0.793  11.583  16173  Z= 0.456
  Chirality :  0.043   0.188   1850
  Planarity :  0.006   0.055   1178
  Dihedral  : 34.586 172.182   3476
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 23.09
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.85 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  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: -0.01 (0.30), residues: 666
  helix:  0.92 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -3.04 (0.35), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS D 109 
 PHE   0.020   0.003   PHE B 100 
 TYR   0.018   0.003   TYR B  88 
 ARG   0.006   0.001   ARG D  86 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9284 (mm) cc_final: 0.8879 (mm)
REVERT: A   63 ARG cc_start: 0.8627 (mmp-170) cc_final: 0.7949 (mmp80)
REVERT: A   70 LEU cc_start: 0.9623 (pp) cc_final: 0.9370 (tt)
REVERT: A   93 GLN cc_start: 0.9115 (tt0) cc_final: 0.8830 (tt0)
REVERT: A  100 LEU cc_start: 0.9345 (tp) cc_final: 0.9131 (tp)
REVERT: A  126 LEU cc_start: 0.9612 (tp) cc_final: 0.9375 (tp)
REVERT: A  128 ARG cc_start: 0.9223 (mtp-110) cc_final: 0.8968 (mmm-85)
REVERT: B   27 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8901 (mp10)
REVERT: C   31 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8028 (ttp80)
REVERT: C   45 ARG cc_start: 0.8349 (mtp-110) cc_final: 0.7994 (mtp-110)
REVERT: C   57 ILE cc_start: 0.9258 (mm) cc_final: 0.9056 (mm)
REVERT: D   42 TYR cc_start: 0.9118 (m-80) cc_final: 0.8915 (m-80)
REVERT: D   80 LEU cc_start: 0.9697 (mt) cc_final: 0.9306 (mt)
REVERT: D   83 TYR cc_start: 0.7864 (m-10) cc_final: 0.7523 (m-80)
REVERT: D  102 LEU cc_start: 0.8399 (tp) cc_final: 0.8130 (tp)
REVERT: E  100 LEU cc_start: 0.9464 (tp) cc_final: 0.9230 (tp)
REVERT: F   88 TYR cc_start: 0.8690 (m-80) cc_final: 0.8229 (m-80)
REVERT: G   31 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8258 (ttp-170)
REVERT: G   59 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8889 (mm-30)
REVERT: H   62 MET cc_start: 0.9365 (tmm) cc_final: 0.9085 (tmm)
REVERT: H   80 LEU cc_start: 0.9648 (mt) cc_final: 0.9328 (mt)
REVERT: H   83 TYR cc_start: 0.7838 (m-10) cc_final: 0.7555 (m-80)
REVERT: H  105 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8621 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2618
  time to fit residues: 60.7427
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.047962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.036219 restraints weight = 82306.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.037377 restraints weight = 45901.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.038147 restraints weight = 31740.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11186  Z= 0.231
  Angle     :  0.688   7.904  16173  Z= 0.402
  Chirality :  0.040   0.239   1850
  Planarity :  0.005   0.059   1178
  Dihedral  : 34.339 174.112   3476
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.10 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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:  0.61 (0.32), residues: 666
  helix:  1.42 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.95 (0.36), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.013   0.002   PHE H  70 
 TYR   0.028   0.002   TYR D  40 
 ARG   0.006   0.001   ARG H  86 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8700 (mmp-170) cc_final: 0.8051 (mmp80)
REVERT: A   70 LEU cc_start: 0.9628 (pp) cc_final: 0.9397 (tt)
REVERT: A   93 GLN cc_start: 0.9159 (tt0) cc_final: 0.8892 (tp40)
REVERT: B   27 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8884 (mp10)
REVERT: B   63 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7950 (mt-10)
REVERT: C   31 ARG cc_start: 0.8501 (ttm170) cc_final: 0.8252 (ttp80)
REVERT: C   57 ILE cc_start: 0.9227 (mm) cc_final: 0.9022 (mm)
REVERT: D  102 LEU cc_start: 0.8338 (tp) cc_final: 0.7934 (tp)
REVERT: D  105 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8672 (tm-30)
REVERT: D  109 HIS cc_start: 0.8842 (m90) cc_final: 0.8356 (m170)
REVERT: E   60 LEU cc_start: 0.8034 (mt) cc_final: 0.7022 (mm)
REVERT: E   97 GLU cc_start: 0.8862 (pm20) cc_final: 0.8206 (pp20)
REVERT: F   58 LEU cc_start: 0.9324 (tt) cc_final: 0.9086 (pp)
REVERT: F   84 MET cc_start: 0.8430 (tpt) cc_final: 0.8027 (tpp)
REVERT: G   31 ARG cc_start: 0.8652 (ttm170) cc_final: 0.7741 (ttp80)
REVERT: G   59 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8822 (mm-30)
REVERT: G   66 LEU cc_start: 0.9033 (mt) cc_final: 0.8692 (pp)
REVERT: H   42 TYR cc_start: 0.9048 (m-80) cc_final: 0.8824 (m-80)
REVERT: H   80 LEU cc_start: 0.9639 (mt) cc_final: 0.9327 (mt)
REVERT: H   83 TYR cc_start: 0.7682 (m-10) cc_final: 0.7376 (m-80)
REVERT: H  102 LEU cc_start: 0.8571 (tp) cc_final: 0.8249 (tp)
REVERT: H  105 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8732 (tm-30)
REVERT: H  109 HIS cc_start: 0.9026 (m170) cc_final: 0.8675 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2625
  time to fit residues: 65.4507
Evaluate side-chains
  148 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
G  35 HIS
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.046509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.035387 restraints weight = 84029.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.036541 restraints weight = 46963.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.037309 restraints weight = 32019.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11186  Z= 0.287
  Angle     :  0.708   7.717  16173  Z= 0.412
  Chirality :  0.040   0.218   1850
  Planarity :  0.005   0.057   1178
  Dihedral  : 34.324 172.300   3476
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 19.55
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  1.95 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  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:  0.53 (0.31), residues: 666
  helix:  1.32 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.85 (0.36), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.019   0.002   PHE E  67 
 TYR   0.037   0.002   TYR H  40 
 ARG   0.005   0.001   ARG H  86 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9303 (mm) cc_final: 0.8925 (mm)
REVERT: A   63 ARG cc_start: 0.8740 (mmp-170) cc_final: 0.8153 (mmp80)
REVERT: A   70 LEU cc_start: 0.9680 (pp) cc_final: 0.9447 (tt)
REVERT: A   93 GLN cc_start: 0.9144 (tt0) cc_final: 0.8776 (tt0)
REVERT: B   27 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8894 (mp10)
REVERT: B   63 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: B   84 MET cc_start: 0.8446 (tpp) cc_final: 0.8169 (tpp)
REVERT: C   31 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8240 (ttp80)
REVERT: C   45 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7823 (mtp-110)
REVERT: C   57 ILE cc_start: 0.9231 (mm) cc_final: 0.9022 (mm)
REVERT: D  102 LEU cc_start: 0.8422 (tp) cc_final: 0.8132 (tp)
REVERT: F   27 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8957 (mp10)
REVERT: F   58 LEU cc_start: 0.9313 (tt) cc_final: 0.9088 (pp)
REVERT: F   63 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: F   84 MET cc_start: 0.8524 (tpt) cc_final: 0.8272 (tpp)
REVERT: G   34 ARG cc_start: 0.9133 (mtp180) cc_final: 0.8755 (mtp180)
REVERT: G   66 LEU cc_start: 0.9062 (mt) cc_final: 0.8755 (pp)
REVERT: H  102 LEU cc_start: 0.8488 (tp) cc_final: 0.8248 (tp)
REVERT: H  105 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8676 (tm-30)
REVERT: H  106 LEU cc_start: 0.9191 (mt) cc_final: 0.8991 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2754
  time to fit residues: 61.0131
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0060
   overall best weight:    1.2200

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 = 0.3351 r_free = 0.3351 target = 0.049082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.037525 restraints weight = 79462.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.038744 restraints weight = 43537.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.039593 restraints weight = 29614.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11186  Z= 0.204
  Angle     :  0.664   8.090  16173  Z= 0.383
  Chirality :  0.039   0.258   1850
  Planarity :  0.005   0.059   1178
  Dihedral  : 34.129 172.819   3476
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.40 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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:  0.88 (0.32), residues: 666
  helix:  1.57 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.71 (0.38), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.011   0.002   PHE A 104 
 TYR   0.024   0.002   TYR F  88 
 ARG   0.006   0.001   ARG A 128 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8194 (mmp80)
REVERT: A   70 LEU cc_start: 0.9674 (pp) cc_final: 0.9436 (tt)
REVERT: A  123 ASP cc_start: 0.9122 (m-30) cc_final: 0.8914 (m-30)
REVERT: A  126 LEU cc_start: 0.9644 (tp) cc_final: 0.9440 (tp)
REVERT: B   27 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8858 (mp10)
REVERT: B   53 GLU cc_start: 0.8084 (mp0) cc_final: 0.7840 (mp0)
REVERT: B   63 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7874 (mt-10)
REVERT: C   57 ILE cc_start: 0.9205 (mm) cc_final: 0.9003 (mm)
REVERT: C   66 LEU cc_start: 0.9049 (mt) cc_final: 0.8569 (pp)
REVERT: D   80 LEU cc_start: 0.9522 (mp) cc_final: 0.9162 (mt)
REVERT: D   83 TYR cc_start: 0.7767 (m-10) cc_final: 0.7564 (m-80)
REVERT: D  102 LEU cc_start: 0.8326 (tp) cc_final: 0.7939 (tp)
REVERT: E  128 ARG cc_start: 0.9480 (mmm-85) cc_final: 0.9192 (mmm-85)
REVERT: F   27 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8945 (mp10)
REVERT: F   58 LEU cc_start: 0.9272 (tt) cc_final: 0.9061 (pp)
REVERT: F   63 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: G   35 HIS cc_start: 0.9029 (m90) cc_final: 0.8567 (m-70)
REVERT: G   46 VAL cc_start: 0.8833 (t) cc_final: 0.8615 (t)
REVERT: G   66 LEU cc_start: 0.9003 (mt) cc_final: 0.8693 (pp)
REVERT: H  102 LEU cc_start: 0.8494 (tp) cc_final: 0.8172 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2349
  time to fit residues: 56.9058
Evaluate side-chains
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 79 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** 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 = 0.047373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.035632 restraints weight = 87999.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.036787 restraints weight = 49663.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.037559 restraints weight = 34260.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.5464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11186  Z= 0.292
  Angle     :  0.698   8.228  16173  Z= 0.404
  Chirality :  0.040   0.256   1850
  Planarity :  0.005   0.054   1178
  Dihedral  : 34.241 171.342   3476
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.25 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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:  0.56 (0.31), residues: 666
  helix:  1.32 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.74 (0.37), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS A 113 
 PHE   0.015   0.002   PHE A 104 
 TYR   0.026   0.002   TYR F  72 
 ARG   0.012   0.001   ARG B  39 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9152 (mm) cc_final: 0.8876 (mm)
REVERT: A   63 ARG cc_start: 0.8626 (mmp-170) cc_final: 0.8021 (mmp80)
REVERT: A   70 LEU cc_start: 0.9676 (pp) cc_final: 0.9381 (tt)
REVERT: A   97 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: A  120 MET cc_start: 0.8817 (tpt) cc_final: 0.8511 (tpt)
REVERT: B   27 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8861 (mp10)
REVERT: B   63 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: C   31 ARG cc_start: 0.8481 (ttm170) cc_final: 0.8232 (ttp80)
REVERT: D  102 LEU cc_start: 0.8522 (tp) cc_final: 0.8166 (tp)
REVERT: F   27 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8879 (mp10)
REVERT: F   58 LEU cc_start: 0.9269 (tt) cc_final: 0.8997 (pp)
REVERT: F   63 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: G  100 ILE cc_start: 0.8832 (mp) cc_final: 0.8618 (mp)
REVERT: H   99 ARG cc_start: 0.9390 (ttm170) cc_final: 0.9096 (ttm-80)
REVERT: H  102 LEU cc_start: 0.8520 (tp) cc_final: 0.8214 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2414
  time to fit residues: 52.4796
Evaluate side-chains
  123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 86 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 = 0.3288 r_free = 0.3288 target = 0.046738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.035283 restraints weight = 84137.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.036457 restraints weight = 46812.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.037252 restraints weight = 31905.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.5717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11186  Z= 0.315
  Angle     :  0.712   8.180  16173  Z= 0.411
  Chirality :  0.040   0.233   1850
  Planarity :  0.005   0.055   1178
  Dihedral  : 34.273 171.961   3476
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 19.92
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.85 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  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:  0.47 (0.31), residues: 666
  helix:  1.26 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -2.85 (0.36), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.023   0.002   PHE E 104 
 TYR   0.025   0.002   TYR D  40 
 ARG   0.007   0.001   ARG A 128 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9145 (mm) cc_final: 0.8752 (mm)
REVERT: A   63 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.7974 (mmp80)
REVERT: A   70 LEU cc_start: 0.9678 (pp) cc_final: 0.9427 (tt)
REVERT: A   97 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7820 (mt-10)
REVERT: A  123 ASP cc_start: 0.9115 (m-30) cc_final: 0.8899 (m-30)
REVERT: A  128 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8882 (mmm-85)
REVERT: B   27 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8852 (mp10)
REVERT: C   31 ARG cc_start: 0.8497 (ttm170) cc_final: 0.8261 (ttp80)
REVERT: D  102 LEU cc_start: 0.8520 (tp) cc_final: 0.8160 (tp)
REVERT: F   27 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8921 (mp10)
REVERT: F   58 LEU cc_start: 0.9272 (tt) cc_final: 0.9013 (pp)
REVERT: G   31 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7632 (ttp-170)
REVERT: G   35 HIS cc_start: 0.8943 (m90) cc_final: 0.8583 (m170)
REVERT: G   66 LEU cc_start: 0.9020 (mt) cc_final: 0.8681 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2563
  time to fit residues: 53.9195
Evaluate side-chains
  118 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 = 0.3287 r_free = 0.3287 target = 0.047009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.036328 restraints weight = 85081.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.037458 restraints weight = 46828.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.038214 restraints weight = 31721.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.5993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11186  Z= 0.260
  Angle     :  0.687   8.445  16173  Z= 0.396
  Chirality :  0.039   0.212   1850
  Planarity :  0.005   0.057   1178
  Dihedral  : 34.194 172.249   3476
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.85 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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:  0.52 (0.31), residues: 666
  helix:  1.28 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.86 (0.37), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.020   0.002   PHE E 104 
 TYR   0.036   0.002   TYR F  88 
 ARG   0.009   0.001   ARG H  99 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9146 (mm) cc_final: 0.8731 (mm)
REVERT: A   63 ARG cc_start: 0.8535 (mmp-170) cc_final: 0.7948 (mmp80)
REVERT: A   70 LEU cc_start: 0.9673 (pp) cc_final: 0.9421 (tt)
REVERT: A   97 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: A  123 ASP cc_start: 0.9058 (m-30) cc_final: 0.8826 (m-30)
REVERT: B   27 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8813 (mp10)
REVERT: B   63 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7960 (mt-10)
REVERT: B   88 TYR cc_start: 0.8604 (m-80) cc_final: 0.8291 (m-80)
REVERT: C   66 LEU cc_start: 0.9063 (mt) cc_final: 0.8619 (pp)
REVERT: D  102 LEU cc_start: 0.8497 (tp) cc_final: 0.8109 (tp)
REVERT: E  120 MET cc_start: 0.8664 (tpp) cc_final: 0.8378 (tpp)
REVERT: F   27 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8864 (mp10)
REVERT: F   58 LEU cc_start: 0.9253 (tt) cc_final: 0.9009 (pp)
REVERT: G   66 LEU cc_start: 0.9010 (mt) cc_final: 0.8672 (pp)
REVERT: H   80 LEU cc_start: 0.9474 (mm) cc_final: 0.9202 (mp)
REVERT: H   83 TYR cc_start: 0.8255 (m-10) cc_final: 0.7829 (m-80)
REVERT: H  102 LEU cc_start: 0.8605 (tp) cc_final: 0.8347 (tp)
REVERT: H  105 GLU cc_start: 0.8838 (pp20) cc_final: 0.8338 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2413
  time to fit residues: 53.2546
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 = 0.050334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.038689 restraints weight = 85098.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.039851 restraints weight = 48931.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040655 restraints weight = 33952.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.6610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11186  Z= 0.193
  Angle     :  0.667   9.263  16173  Z= 0.377
  Chirality :  0.038   0.231   1850
  Planarity :  0.005   0.065   1178
  Dihedral  : 33.905 171.912   3476
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  2.70 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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:  0.80 (0.32), residues: 666
  helix:  1.42 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.39 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.015   0.001   PHE E 104 
 TYR   0.016   0.002   TYR H  40 
 ARG   0.007   0.001   ARG H  99 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8475 (mt) cc_final: 0.8137 (mp)
REVERT: A   62 ILE cc_start: 0.9148 (mm) cc_final: 0.8781 (mm)
REVERT: A   63 ARG cc_start: 0.8520 (mmp-170) cc_final: 0.7963 (mmp80)
REVERT: A   70 LEU cc_start: 0.9655 (pp) cc_final: 0.9389 (tt)
REVERT: A   97 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: A  123 ASP cc_start: 0.8999 (m-30) cc_final: 0.8763 (m-30)
REVERT: B   27 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8771 (mp10)
REVERT: B   50 ILE cc_start: 0.8730 (mt) cc_final: 0.8479 (mm)
REVERT: B   63 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: B   85 ASP cc_start: 0.9024 (m-30) cc_final: 0.8819 (m-30)
REVERT: B   88 TYR cc_start: 0.8349 (m-80) cc_final: 0.8088 (m-80)
REVERT: C   31 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.7403 (ttp80)
REVERT: C   66 LEU cc_start: 0.8968 (mt) cc_final: 0.8619 (pp)
REVERT: D   37 TYR cc_start: 0.8560 (m-80) cc_final: 0.8199 (m-80)
REVERT: D  102 LEU cc_start: 0.8380 (tp) cc_final: 0.7842 (tp)
REVERT: E  120 MET cc_start: 0.8704 (tpp) cc_final: 0.8405 (tpp)
REVERT: F   27 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8868 (mp10)
REVERT: G   66 LEU cc_start: 0.9028 (mt) cc_final: 0.8683 (pp)
REVERT: H   80 LEU cc_start: 0.9505 (mm) cc_final: 0.9109 (mm)
REVERT: H   83 TYR cc_start: 0.8089 (m-10) cc_final: 0.7733 (m-80)
REVERT: H  102 LEU cc_start: 0.8478 (tp) cc_final: 0.8157 (tp)
REVERT: H  105 GLU cc_start: 0.8649 (pp20) cc_final: 0.8418 (pm20)
REVERT: H  106 LEU cc_start: 0.8937 (mt) cc_final: 0.8707 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2438
  time to fit residues: 59.5096
Evaluate side-chains
  136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 70 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0770
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   overall best weight:    4.0146

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  21 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.046812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.035462 restraints weight = 88375.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.036507 restraints weight = 51474.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.037220 restraints weight = 36383.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.6481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11186  Z= 0.346
  Angle     :  0.723   8.200  16173  Z= 0.417
  Chirality :  0.040   0.215   1850
  Planarity :  0.006   0.077   1178
  Dihedral  : 34.120 171.102   3476
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 20.77
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  2.70 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.59 (0.31), residues: 666
  helix:  1.29 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -2.49 (0.40), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 113 
 PHE   0.018   0.002   PHE E 104 
 TYR   0.018   0.002   TYR H  40 
 ARG   0.010   0.001   ARG A 128 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2601.74 seconds
wall clock time: 47 minutes 43.16 seconds (2863.16 seconds total)