Starting phenix.real_space_refine
on Wed Feb  4 16:55:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k46_62048/02_2026/9k46_62048.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.004 sd=   0.051
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     289      5.49       5
     S      14      5.16       5
     C    6597      2.51       5
     N    2172      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11844
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.36, per 1000 atoms: 0.20
  Number of scatterers: 11844
  At special positions: 0
  Unit cell: (123.28, 80.4, 115.776, 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     289     15.00
     O    2772      8.00
     N    2172      7.00
     C    6597      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 310.0 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      72.4% alpha, 3.2% beta
      144 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.590A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 25 through 30
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 98
    Processing helix  chain 'C' and resid 99 through 106
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 127 through 147
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.587A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 98
    Processing helix  chain 'G' and resid 99 through 106
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 127 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.090A  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 'B' and resid 96 through 98
      removed outlier: 6.824A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.224A  pdb=" N   ARG C  51 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.149A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 52
      removed outlier: 7.123A  pdb=" N   ARG G  51 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87

    408 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      346 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.14 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: 2001
        1.33 -     1.45: 4263
        1.45 -     1.57: 5784
        1.57 -     1.69: 577
        1.69 -     1.81: 26
  Bond restraints: 12651
  Sorted by residual:
  bond pdb=" O3'  DG I -26 "
       pdb=" P    DT I -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.668 -0.061 1.50e-02 4.44e+03 1.64e+01
  bond pdb=" O3'  DT J -36 "
       pdb=" P    DG J -35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.658 -0.051 1.50e-02 4.44e+03 1.18e+01
  bond pdb=" O3'  DC J -24 "
       pdb=" P    DC J -23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.655 -0.048 1.50e-02 4.44e+03 1.04e+01
  bond pdb=" O3'  DA J  46 "
       pdb=" P    DT J  47 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.26e+00
  bond pdb=" O3'  DC I  12 "
       pdb=" P    DT I  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.646 -0.039 1.50e-02 4.44e+03 6.85e+00
  ... (remaining 12646 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 17660
        1.45 -     2.91: 607
        2.91 -     4.36: 49
        4.36 -     5.82: 8
        5.82 -     7.27: 1
  Bond angle restraints: 18325
  Sorted by residual:
  angle pdb=" O3'  DG J -27 "
        pdb=" C3'  DG J -27 "
        pdb=" C2'  DG J -27 "
      ideal   model   delta    sigma   weight residual
     111.50  104.23    7.27 1.50e+00 4.44e-01 2.35e+01
  angle pdb=" O3'  DG J -38 "
        pdb=" C3'  DG J -38 "
        pdb=" C2'  DG J -38 "
      ideal   model   delta    sigma   weight residual
     111.50  106.59    4.91 1.50e+00 4.44e-01 1.07e+01
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  106.73    4.77 1.50e+00 4.44e-01 1.01e+01
  angle pdb=" O3'  DA I  -8 "
        pdb=" C3'  DA I  -8 "
        pdb=" C2'  DA I  -8 "
      ideal   model   delta    sigma   weight residual
     111.50  106.78    4.72 1.50e+00 4.44e-01 9.89e+00
  angle pdb=" O3'  DC J  44 "
        pdb=" C3'  DC J  44 "
        pdb=" C2'  DC J  44 "
      ideal   model   delta    sigma   weight residual
     111.50  107.03    4.47 1.50e+00 4.44e-01 8.88e+00
  ... (remaining 18320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.36: 4612
       23.36 -    46.72: 1515
       46.72 -    70.08: 789
       70.08 -    93.44: 26
       93.44 -   116.80: 1
  Dihedral angle restraints: 6943
    sinusoidal: 4791
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" C4'  DG J -17 "
           pdb=" C3'  DG J -17 "
           pdb=" O3'  DG J -17 "
           pdb=" P    DC J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -23.20 -116.80     1      3.50e+01 8.16e-04 1.14e+01
  dihedral pdb=" CG  ARG E  49 "
           pdb=" CD  ARG E  49 "
           pdb=" NE  ARG E  49 "
           pdb=" CZ  ARG E  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.26   42.74     2      1.50e+01 4.44e-03 9.83e+00
  dihedral pdb=" CG  ARG G  97 "
           pdb=" CD  ARG G  97 "
           pdb=" NE  ARG G  97 "
           pdb=" CZ  ARG G  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.43  -42.57     2      1.50e+01 4.44e-03 9.76e+00
  ... (remaining 6940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1661
       0.042 -    0.085: 338
       0.085 -    0.127: 73
       0.127 -    0.170: 12
       0.170 -    0.212: 5
  Chirality restraints: 2089
  Sorted by residual:
  chirality pdb=" C3'  DG J -27 "
            pdb=" C4'  DG J -27 "
            pdb=" O3'  DG J -27 "
            pdb=" C2'  DG J -27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C3'  DA I  -8 "
            pdb=" C4'  DA I  -8 "
            pdb=" O3'  DA I  -8 "
            pdb=" C2'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C3'  DT I  13 "
            pdb=" C4'  DT I  13 "
            pdb=" O3'  DT I  13 "
            pdb=" C2'  DT I  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 8.78e-01
  ... (remaining 2086 not shown)

  Planarity restraints: 1306
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  59 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   LYS B  59 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LYS B  59 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B  60 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.55e+00
        pdb=" C   LYS F  59 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE F  60 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F  52 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" CD  GLU F  52 "    0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLU F  52 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU F  52 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1303 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 910
        2.74 -     3.28: 10492
        3.28 -     3.82: 23150
        3.82 -     4.36: 28452
        4.36 -     4.90: 40346
  Nonbonded interactions: 103350
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C  41 "
            pdb=" OE1 GLU D  58 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   ASN G  82 "
            pdb=" ND2 ASN G  82 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   ASN C  82 "
            pdb=" ND2 ASN C  82 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OH  TYR C  48 "
            pdb=" OE2 GLU D  94 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.250 3.040
  ... (remaining 103345 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=0.00 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:             1.000
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.340
  Find NCS groups from input model:        0.060
  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:5.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  12651  Z= 0.184
  Angle     :  0.590   7.273  18325  Z= 0.368
  Chirality :  0.038   0.212   2089
  Planarity :  0.004   0.034   1306
  Dihedral  : 29.027 116.802   5555
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 20.67 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.30), residues: 730
  helix:  1.32 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.06 (0.40), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  41 
 TYR   0.016   0.001   TYR H  63 
 PHE   0.006   0.001   PHE G  34 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12651)
  covalent geometry    : angle       0.58979 (18325)
  hydrogen bonds       : bond        0.12183 (  754)
  hydrogen bonds       : angle       5.19157 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 178
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8470 (tt0) cc_final: 0.7793 (tt0)
REVERT: C  121 ASN cc_start: 0.9122 (t0) cc_final: 0.8887 (t0)
REVERT: D   56 ASN cc_start: 0.9292 (m-40) cc_final: 0.8927 (m-40)
REVERT: D   91 ASP cc_start: 0.8784 (t0) cc_final: 0.8551 (t0)
REVERT: E   73 GLU cc_start: 0.8338 (tt0) cc_final: 0.7702 (tt0)
REVERT: F   27 GLN cc_start: 0.9224 (tp40) cc_final: 0.9007 (mp10)
REVERT: G  121 ASN cc_start: 0.9198 (t0) cc_final: 0.8962 (t0)
REVERT: H   56 ASN cc_start: 0.8899 (m-40) cc_final: 0.8516 (m-40)
REVERT: H   91 ASP cc_start: 0.8689 (t0) cc_final: 0.8483 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 181
  average time/residue: 0.7790
  time to fit residues: 149.0538
Evaluate side-chains
  147 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   49 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** C  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
D 132 HIS
G  82 ASN
G 119 ASN
H 132 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.063664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042196 restraints weight = 41146.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 1.95
r_work: 0.2585 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  12651  Z= 0.213
  Angle     :  0.588   7.595  18325  Z= 0.357
  Chirality :  0.035   0.120   2089
  Planarity :  0.004   0.035   1306
  Dihedral  : 31.374 109.411   4082
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.68 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.30), residues: 730
  helix:  2.42 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.06 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  80 
 TYR   0.015   0.002   TYR H  63 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (12651)
  covalent geometry    : angle       0.58842 (18325)
  hydrogen bonds       : bond        0.04497 (  754)
  hydrogen bonds       : angle       2.91673 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8763 (pm20) cc_final: 0.7673 (pm20)
REVERT: A   73 GLU cc_start: 0.8768 (tt0) cc_final: 0.8383 (tt0)
REVERT: A  106 ASP cc_start: 0.8985 (m-30) cc_final: 0.8741 (m-30)
REVERT: C   99 ASP cc_start: 0.8964 (t0) cc_final: 0.8467 (t0)
REVERT: C  101 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8950 (mm-30)
REVERT: C  104 LYS cc_start: 0.9595 (ttpt) cc_final: 0.9376 (ttmm)
REVERT: C  121 ASN cc_start: 0.8845 (t0) cc_final: 0.8486 (t0)
REVERT: D   56 ASN cc_start: 0.9094 (m-40) cc_final: 0.8704 (m-40)
REVERT: D   91 ASP cc_start: 0.9322 (t0) cc_final: 0.8929 (t0)
REVERT: D  128 GLU cc_start: 0.8640 (tp30) cc_final: 0.8209 (mm-30)
REVERT: D  135 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9148 (p)
REVERT: E   73 GLU cc_start: 0.8810 (tt0) cc_final: 0.8459 (tt0)
REVERT: F   27 GLN cc_start: 0.9480 (tp40) cc_final: 0.9081 (mp10)
REVERT: G   83 LYS cc_start: 0.9354 (mmtp) cc_final: 0.9125 (mmmm)
REVERT: G   99 ASP cc_start: 0.8839 (t0) cc_final: 0.8505 (t0)
REVERT: G  101 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8669 (mt-10)
REVERT: G  104 LYS cc_start: 0.9566 (ttpt) cc_final: 0.9325 (ttmm)
REVERT: G  121 ASN cc_start: 0.8888 (t0) cc_final: 0.8533 (t0)
REVERT: H   56 ASN cc_start: 0.8690 (m-40) cc_final: 0.8402 (m-40)
REVERT: H   70 GLN cc_start: 0.9240 (tt0) cc_final: 0.9028 (tt0)
REVERT: H  106 TYR cc_start: 0.8503 (m-10) cc_final: 0.7862 (m-80)
REVERT: H  128 GLU cc_start: 0.8545 (tp30) cc_final: 0.8249 (mm-30)
  outliers start: 18
  outliers final: 2
  residues processed: 174
  average time/residue: 0.7572
  time to fit residues: 139.2309
Evaluate side-chains
  155 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 152
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain H residue   85 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 52 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
G  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.062151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.040810 restraints weight = 42014.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 1.97
r_work: 0.2548 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12651  Z= 0.235
  Angle     :  0.611   8.879  18325  Z= 0.362
  Chirality :  0.036   0.205   2089
  Planarity :  0.004   0.031   1306
  Dihedral  : 31.547 104.755   4073
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 25.16 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.31), residues: 730
  helix:  2.79 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.04 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 105 
 TYR   0.014   0.002   TYR H  63 
 PHE   0.007   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (12651)
  covalent geometry    : angle       0.61064 (18325)
  hydrogen bonds       : bond        0.04453 (  754)
  hydrogen bonds       : angle       2.88538 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8300 (pm20)
REVERT: C   99 ASP cc_start: 0.9013 (t0) cc_final: 0.8524 (t0)
REVERT: C  101 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8941 (mm-30)
REVERT: C  104 LYS cc_start: 0.9569 (ttpt) cc_final: 0.9339 (ttmm)
REVERT: C  121 ASN cc_start: 0.8921 (t0) cc_final: 0.8623 (t0)
REVERT: D   56 ASN cc_start: 0.9056 (m-40) cc_final: 0.8708 (m-40)
REVERT: D   82 MET cc_start: 0.9510 (tpp) cc_final: 0.9293 (tpp)
REVERT: D   91 ASP cc_start: 0.9268 (t0) cc_final: 0.8858 (t0)
REVERT: D  128 GLU cc_start: 0.8722 (tp30) cc_final: 0.8309 (mm-30)
REVERT: D  135 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9182 (p)
REVERT: E   59 GLU cc_start: 0.8568 (pm20) cc_final: 0.8313 (pm20)
REVERT: F   27 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.9189 (mp10)
REVERT: F   85 ASP cc_start: 0.9308 (m-30) cc_final: 0.9087 (m-30)
REVERT: G   83 LYS cc_start: 0.9353 (mmtp) cc_final: 0.9094 (mmmm)
REVERT: G   99 ASP cc_start: 0.8996 (t0) cc_final: 0.8568 (t0)
REVERT: G  101 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8548 (mt-10)
REVERT: G  104 LYS cc_start: 0.9556 (ttpt) cc_final: 0.9319 (ttmm)
REVERT: G  121 ASN cc_start: 0.8965 (t0) cc_final: 0.8456 (t0)
REVERT: H   70 GLN cc_start: 0.9299 (tt0) cc_final: 0.9099 (tt0)
REVERT: H   82 MET cc_start: 0.9507 (tpp) cc_final: 0.9278 (tpp)
REVERT: H  109 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (tttm)
REVERT: H  128 GLU cc_start: 0.8636 (tp30) cc_final: 0.8321 (mm-30)
  outliers start: 16
  outliers final: 3
  residues processed: 160
  average time/residue: 0.7599
  time to fit residues: 128.3726
Evaluate side-chains
  152 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 146
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 44 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.062469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.040983 restraints weight = 41441.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 1.98
r_work: 0.2573 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12651  Z= 0.189
  Angle     :  0.577   9.497  18325  Z= 0.347
  Chirality :  0.034   0.123   2089
  Planarity :  0.004   0.031   1306
  Dihedral  : 31.229 101.089   4073
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 25.32 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.50 (0.31), residues: 730
  helix:  2.96 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.10 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  80 
 TYR   0.012   0.001   TYR H  63 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (12651)
  covalent geometry    : angle       0.57682 (18325)
  hydrogen bonds       : bond        0.03861 (  754)
  hydrogen bonds       : angle       2.67715 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8713 (pm20) cc_final: 0.8473 (pm20)
REVERT: B   85 ASP cc_start: 0.9288 (m-30) cc_final: 0.9080 (m-30)
REVERT: B   96 THR cc_start: 0.9647 (m) cc_final: 0.9137 (p)
REVERT: C   99 ASP cc_start: 0.9060 (t0) cc_final: 0.8595 (t0)
REVERT: C  104 LYS cc_start: 0.9574 (ttpt) cc_final: 0.9336 (ttmm)
REVERT: C  121 ASN cc_start: 0.8884 (t0) cc_final: 0.8612 (t0)
REVERT: D   56 ASN cc_start: 0.8991 (m-40) cc_final: 0.8708 (m-40)
REVERT: D   91 ASP cc_start: 0.9239 (t0) cc_final: 0.8800 (t0)
REVERT: D  128 GLU cc_start: 0.8654 (tp30) cc_final: 0.8247 (mm-30)
REVERT: D  135 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9166 (p)
REVERT: E   59 GLU cc_start: 0.8509 (pm20) cc_final: 0.8211 (pm20)
REVERT: F   27 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9149 (mp10)
REVERT: G   83 LYS cc_start: 0.9354 (mmtp) cc_final: 0.9084 (mmmm)
REVERT: G   99 ASP cc_start: 0.8960 (t0) cc_final: 0.8509 (t0)
REVERT: G  104 LYS cc_start: 0.9547 (ttpt) cc_final: 0.9315 (ttmm)
REVERT: G  121 ASN cc_start: 0.8937 (t0) cc_final: 0.8392 (t0)
REVERT: H   58 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (mm-30)
REVERT: H   70 GLN cc_start: 0.9314 (tt0) cc_final: 0.9114 (tt0)
REVERT: H   82 MET cc_start: 0.9463 (tpp) cc_final: 0.9227 (tpp)
REVERT: H  109 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8484 (tttm)
REVERT: H  128 GLU cc_start: 0.8603 (tp30) cc_final: 0.8341 (mm-30)
  outliers start: 16
  outliers final: 5
  residues processed: 160
  average time/residue: 0.7755
  time to fit residues: 130.9939
Evaluate side-chains
  154 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   58 GLU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
H 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.063483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.042572 restraints weight = 41513.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 1.96
r_work: 0.2612 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12651  Z= 0.155
  Angle     :  0.569  10.553  18325  Z= 0.342
  Chirality :  0.033   0.122   2089
  Planarity :  0.004   0.034   1306
  Dihedral  : 30.975  98.260   4073
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 26.44 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.57 (0.30), residues: 730
  helix:  3.02 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.10 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  80 
 TYR   0.013   0.001   TYR H  63 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12651)
  covalent geometry    : angle       0.56856 (18325)
  hydrogen bonds       : bond        0.03408 (  754)
  hydrogen bonds       : angle       2.54281 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8958 (tt0) cc_final: 0.8416 (tt0)
REVERT: B   85 ASP cc_start: 0.9153 (m-30) cc_final: 0.8946 (m-30)
REVERT: B   96 THR cc_start: 0.9652 (m) cc_final: 0.9206 (p)
REVERT: C   99 ASP cc_start: 0.9017 (t0) cc_final: 0.8518 (t0)
REVERT: C  104 LYS cc_start: 0.9584 (ttpt) cc_final: 0.9341 (ttmm)
REVERT: C  121 ASN cc_start: 0.8833 (t0) cc_final: 0.8365 (t0)
REVERT: D   91 ASP cc_start: 0.9237 (t0) cc_final: 0.8787 (t0)
REVERT: D  128 GLU cc_start: 0.8662 (tp30) cc_final: 0.8280 (mm-30)
REVERT: E   59 GLU cc_start: 0.8520 (pm20) cc_final: 0.8236 (pm20)
REVERT: E   73 GLU cc_start: 0.9058 (tt0) cc_final: 0.8737 (tt0)
REVERT: F   23 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7664 (mmm160)
REVERT: F   27 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9159 (mp10)
REVERT: F   96 THR cc_start: 0.9644 (m) cc_final: 0.9241 (p)
REVERT: G   83 LYS cc_start: 0.9329 (mmtp) cc_final: 0.9063 (mmmm)
REVERT: G   99 ASP cc_start: 0.8906 (t0) cc_final: 0.8476 (t0)
REVERT: G  104 LYS cc_start: 0.9537 (ttpt) cc_final: 0.9311 (ttmm)
REVERT: H   82 MET cc_start: 0.9383 (tpp) cc_final: 0.9154 (tpp)
REVERT: H  109 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8114 (mptt)
REVERT: H  116 GLU cc_start: 0.8988 (mp0) cc_final: 0.8374 (mp0)
REVERT: H  128 GLU cc_start: 0.8581 (tp30) cc_final: 0.8312 (mm-30)
  outliers start: 17
  outliers final: 5
  residues processed: 164
  average time/residue: 0.7495
  time to fit residues: 129.7379
Evaluate side-chains
  153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.061979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.040927 restraints weight = 41930.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 1.99
r_work: 0.2559 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12651  Z= 0.196
  Angle     :  0.587  11.206  18325  Z= 0.351
  Chirality :  0.034   0.129   2089
  Planarity :  0.004   0.035   1306
  Dihedral  : 31.123  93.659   4073
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 27.24 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.49 (0.30), residues: 730
  helix:  2.98 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.00 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  80 
 TYR   0.010   0.002   TYR H  63 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12651)
  covalent geometry    : angle       0.58662 (18325)
  hydrogen bonds       : bond        0.04059 (  754)
  hydrogen bonds       : angle       2.66581 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9003 (tt0) cc_final: 0.8375 (tt0)
REVERT: B   85 ASP cc_start: 0.9164 (m-30) cc_final: 0.8934 (m-30)
REVERT: C   83 LYS cc_start: 0.9384 (mppt) cc_final: 0.9109 (mmmm)
REVERT: C   99 ASP cc_start: 0.9046 (t0) cc_final: 0.8620 (t0)
REVERT: C  104 LYS cc_start: 0.9572 (ttpt) cc_final: 0.9335 (ttmm)
REVERT: C  121 ASN cc_start: 0.8935 (t0) cc_final: 0.8454 (t0)
REVERT: D   91 ASP cc_start: 0.9324 (t0) cc_final: 0.8875 (t0)
REVERT: D  128 GLU cc_start: 0.8732 (tp30) cc_final: 0.8319 (mm-30)
REVERT: E   59 GLU cc_start: 0.8522 (pm20) cc_final: 0.8212 (pm20)
REVERT: E   73 GLU cc_start: 0.9040 (tt0) cc_final: 0.8615 (tt0)
REVERT: F   27 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.9134 (mp10)
REVERT: G   83 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9096 (mmmm)
REVERT: G   99 ASP cc_start: 0.9002 (t0) cc_final: 0.8506 (t0)
REVERT: G  104 LYS cc_start: 0.9560 (ttpt) cc_final: 0.9315 (ttmm)
REVERT: H   82 MET cc_start: 0.9407 (tpp) cc_final: 0.9179 (tpp)
REVERT: H  106 TYR cc_start: 0.8352 (m-10) cc_final: 0.7977 (m-80)
REVERT: H  109 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8525 (tttm)
REVERT: H  128 GLU cc_start: 0.8700 (tp30) cc_final: 0.8366 (mm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 155
  average time/residue: 0.7643
  time to fit residues: 124.9921
Evaluate side-chains
  156 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
E 113 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.060310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.039382 restraints weight = 42032.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 2.02
r_work: 0.2525 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12651  Z= 0.232
  Angle     :  0.611  12.483  18325  Z= 0.362
  Chirality :  0.036   0.120   2089
  Planarity :  0.004   0.034   1306
  Dihedral  : 31.326  91.513   4073
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 28.85 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.40 (0.30), residues: 730
  helix:  2.92 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.09 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 105 
 TYR   0.012   0.002   TYR F  88 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (12651)
  covalent geometry    : angle       0.61100 (18325)
  hydrogen bonds       : bond        0.04348 (  754)
  hydrogen bonds       : angle       2.77358 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8884 (tt0) cc_final: 0.8584 (tt0)
REVERT: B   24 ASP cc_start: 0.8245 (t0) cc_final: 0.8040 (t0)
REVERT: B   85 ASP cc_start: 0.9349 (m-30) cc_final: 0.9114 (m-30)
REVERT: C   83 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9102 (mmmm)
REVERT: C   99 ASP cc_start: 0.9039 (t0) cc_final: 0.8659 (t0)
REVERT: C  104 LYS cc_start: 0.9584 (ttpt) cc_final: 0.9361 (ttmm)
REVERT: C  121 ASN cc_start: 0.9065 (t0) cc_final: 0.8644 (t0)
REVERT: D   91 ASP cc_start: 0.9353 (t0) cc_final: 0.8932 (t0)
REVERT: D   99 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8982 (tp30)
REVERT: D  128 GLU cc_start: 0.8776 (tp30) cc_final: 0.8380 (mm-30)
REVERT: D  135 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9186 (p)
REVERT: E   59 GLU cc_start: 0.8552 (pm20) cc_final: 0.8226 (pm20)
REVERT: E   73 GLU cc_start: 0.9067 (tt0) cc_final: 0.8709 (tt0)
REVERT: F   27 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9125 (mp10)
REVERT: G   83 LYS cc_start: 0.9379 (mmtp) cc_final: 0.9109 (mmmm)
REVERT: G   99 ASP cc_start: 0.9072 (t0) cc_final: 0.8604 (t0)
REVERT: G  104 LYS cc_start: 0.9578 (ttpt) cc_final: 0.9354 (ttmm)
REVERT: G  121 ASN cc_start: 0.9069 (t0) cc_final: 0.8633 (t0)
REVERT: H   82 MET cc_start: 0.9429 (tpp) cc_final: 0.9193 (tpp)
REVERT: H   91 ASP cc_start: 0.9264 (t0) cc_final: 0.8856 (t0)
REVERT: H  109 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8656 (tttm)
REVERT: H  128 GLU cc_start: 0.8742 (tp30) cc_final: 0.8376 (mm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 154
  average time/residue: 0.8292
  time to fit residues: 134.8385
Evaluate side-chains
  156 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   83 LYS
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0070
   overall best weight:    1.3602

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

Flipped N/Q/H residues before XYZ refinement:
D 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.061273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.040556 restraints weight = 41858.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 2.01
r_work: 0.2565 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12651  Z= 0.175
  Angle     :  0.594  12.579  18325  Z= 0.352
  Chirality :  0.034   0.117   2089
  Planarity :  0.004   0.063   1306
  Dihedral  : 31.043  90.437   4073
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 29.01 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.46 (0.30), residues: 730
  helix:  2.99 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.15 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  23 
 TYR   0.016   0.002   TYR H 106 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12651)
  covalent geometry    : angle       0.59407 (18325)
  hydrogen bonds       : bond        0.03618 (  754)
  hydrogen bonds       : angle       2.60389 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7953 (tpm-80)
REVERT: B   85 ASP cc_start: 0.9265 (m-30) cc_final: 0.9048 (m-30)
REVERT: B   96 THR cc_start: 0.9676 (m) cc_final: 0.9196 (p)
REVERT: C   83 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9117 (mmmm)
REVERT: C   99 ASP cc_start: 0.9012 (t0) cc_final: 0.8660 (t0)
REVERT: C  104 LYS cc_start: 0.9582 (ttpt) cc_final: 0.9342 (ttmm)
REVERT: C  121 ASN cc_start: 0.9085 (t0) cc_final: 0.8594 (t0)
REVERT: D   91 ASP cc_start: 0.9314 (t0) cc_final: 0.8869 (t0)
REVERT: D   99 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8971 (tp30)
REVERT: D  128 GLU cc_start: 0.8738 (tp30) cc_final: 0.8355 (mm-30)
REVERT: E   59 GLU cc_start: 0.8526 (pm20) cc_final: 0.8205 (pm20)
REVERT: E   73 GLU cc_start: 0.8919 (tt0) cc_final: 0.8650 (tt0)
REVERT: G   83 LYS cc_start: 0.9367 (mmtp) cc_final: 0.9102 (mmmm)
REVERT: G   99 ASP cc_start: 0.9018 (t0) cc_final: 0.8582 (t0)
REVERT: G  104 LYS cc_start: 0.9565 (ttpt) cc_final: 0.9338 (ttmm)
REVERT: G  121 ASN cc_start: 0.9013 (t0) cc_final: 0.8589 (t0)
REVERT: H  109 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8499 (tttm)
REVERT: H  128 GLU cc_start: 0.8665 (tp30) cc_final: 0.8339 (mm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 162
  average time/residue: 0.8198
  time to fit residues: 140.3485
Evaluate side-chains
  157 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   83 LYS
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.060968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.040183 restraints weight = 41624.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 2.02
r_work: 0.2554 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12651  Z= 0.191
  Angle     :  0.608  13.600  18325  Z= 0.358
  Chirality :  0.034   0.137   2089
  Planarity :  0.004   0.054   1306
  Dihedral  : 31.105  88.778   4073
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 29.81 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.47 (0.30), residues: 730
  helix:  3.00 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.16 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  23 
 TYR   0.014   0.002   TYR H 106 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (12651)
  covalent geometry    : angle       0.60818 (18325)
  hydrogen bonds       : bond        0.03818 (  754)
  hydrogen bonds       : angle       2.62766 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.9252 (m-30) cc_final: 0.9024 (m-30)
REVERT: C   83 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9123 (mmmm)
REVERT: C   99 ASP cc_start: 0.9015 (t0) cc_final: 0.8637 (t0)
REVERT: C  104 LYS cc_start: 0.9577 (ttpt) cc_final: 0.9337 (ttmm)
REVERT: C  121 ASN cc_start: 0.9042 (t0) cc_final: 0.8548 (t0)
REVERT: D   91 ASP cc_start: 0.9317 (t0) cc_final: 0.8872 (t0)
REVERT: D   99 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8999 (tp30)
REVERT: D  128 GLU cc_start: 0.8766 (tp30) cc_final: 0.8363 (mm-30)
REVERT: E   59 GLU cc_start: 0.8513 (pm20) cc_final: 0.8161 (pm20)
REVERT: E   73 GLU cc_start: 0.8916 (tt0) cc_final: 0.8645 (tt0)
REVERT: G   83 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9101 (mmmm)
REVERT: G   99 ASP cc_start: 0.9049 (t0) cc_final: 0.8605 (t0)
REVERT: G  104 LYS cc_start: 0.9561 (ttpt) cc_final: 0.9335 (ttmm)
REVERT: G  121 ASN cc_start: 0.8979 (t0) cc_final: 0.8546 (t0)
REVERT: H  109 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (tttm)
REVERT: H  128 GLU cc_start: 0.8691 (tp30) cc_final: 0.8354 (mm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 159
  average time/residue: 0.8667
  time to fit residues: 145.4185
Evaluate side-chains
  158 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   83 LYS
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.059650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.038794 restraints weight = 42022.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.2690 rms_B_bonded: 2.01
r_work: 0.2506 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  12651  Z= 0.257
  Angle     :  0.643  14.665  18325  Z= 0.376
  Chirality :  0.036   0.120   2089
  Planarity :  0.005   0.047   1306
  Dihedral  : 31.410  89.130   4073
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 29.33 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.30), residues: 730
  helix:  2.89 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.31 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 105 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.002   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (12651)
  covalent geometry    : angle       0.64308 (18325)
  hydrogen bonds       : bond        0.04555 (  754)
  hydrogen bonds       : angle       2.83707 ( 1898)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   83 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9109 (mmmm)
REVERT: C   99 ASP cc_start: 0.9028 (t0) cc_final: 0.8681 (t0)
REVERT: C  104 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9362 (ttmm)
REVERT: C  121 ASN cc_start: 0.9079 (t0) cc_final: 0.8651 (t0)
REVERT: D   91 ASP cc_start: 0.9361 (t0) cc_final: 0.8946 (t0)
REVERT: D   99 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9038 (tp30)
REVERT: D  128 GLU cc_start: 0.8810 (tp30) cc_final: 0.8393 (mm-30)
REVERT: E   59 GLU cc_start: 0.8567 (pm20) cc_final: 0.8236 (pm20)
REVERT: E   73 GLU cc_start: 0.8965 (tt0) cc_final: 0.8728 (tt0)
REVERT: G   83 LYS cc_start: 0.9380 (mmtp) cc_final: 0.9106 (mmmm)
REVERT: G   99 ASP cc_start: 0.9077 (t0) cc_final: 0.8648 (t0)
REVERT: G  104 LYS cc_start: 0.9572 (ttpt) cc_final: 0.9352 (ttmm)
REVERT: G  121 ASN cc_start: 0.9067 (t0) cc_final: 0.8633 (t0)
REVERT: H   91 ASP cc_start: 0.9301 (t0) cc_final: 0.8930 (t0)
REVERT: H  109 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8689 (tttm)
REVERT: H  128 GLU cc_start: 0.8767 (tp30) cc_final: 0.8390 (mm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 155
  average time/residue: 0.8574
  time to fit residues: 140.1428
Evaluate side-chains
  154 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   83 LYS
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   85 MET
Chi-restraints excluded: chain H residue  109 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 88 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.059402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.038868 restraints weight = 41643.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.2693 rms_B_bonded: 1.98
r_work: 0.2511 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  12651  Z= 0.249
  Angle     :  0.653  14.295  18325  Z= 0.378
  Chirality :  0.036   0.119   2089
  Planarity :  0.004   0.043   1306
  Dihedral  : 31.302  89.193   4073
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 30.77 %
    Favored  : 67.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.31), residues: 730
  helix:  2.92 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.34 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 105 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (12651)
  covalent geometry    : angle       0.65276 (18325)
  hydrogen bonds       : bond        0.04294 (  754)
  hydrogen bonds       : angle       2.76335 ( 1898)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3734.19 seconds
wall clock time: 64 minutes 8.23 seconds (3848.23 seconds total)