Starting phenix.real_space_refine
on Wed Feb  4 02:48:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qv7_53388/02_2026/9qv7_53388.map"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.002
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     240      5.49       5
     S      12      5.16       5
     C    4551      2.51       5
     N    1659      2.21       5
     O    2166      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 8628
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "B"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "C"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "D"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "E"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "F"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "G"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 273
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 63}
          Link IDs: {'TRANS': 67}
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 371
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "H"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 273
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 63}
          Link IDs: {'TRANS': 67}
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 371
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "X"
      Number of atoms: 2446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 2446
          Classifications: {'DNA': 120}
          Link IDs: {'rna3p': 119}
    Chain: "Y"
      Number of atoms: 2474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 2474
          Classifications: {'DNA': 120}
          Link IDs: {'rna3p': 119}
  Time building chain proxies: 1.48, per 1000 atoms: 0.17
  Number of scatterers: 8628
  At special positions: 0
  Unit cell: (147.825, 109.865, 109.865, 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      12     16.00
     P     240     15.00
     O    2166      8.00
     N    1659      7.00
     C    4551      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: 0.43
  Conformation dependent library (CDL) restraints added in 118.2 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      79.0% alpha, 2.9% beta
      90 base pairs and 183 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 23 through 53
    Processing helix  chain 'A' and resid 58 through 67
      removed outlier: 3.592A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 18
      removed outlier: 3.514A  pdb=" N   GLY B  18 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 53
    Processing helix  chain 'B' and resid 58 through 67
      removed outlier: 3.589A  pdb=" N   ILE B  62 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 18
      removed outlier: 3.502A  pdb=" N   LEU C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 53
    Processing helix  chain 'C' and resid 58 through 66
    Processing helix  chain 'D' and resid 6 through 18
    Processing helix  chain 'D' and resid 23 through 53
    Processing helix  chain 'D' and resid 58 through 67
    Processing helix  chain 'E' and resid 6 through 18
    Processing helix  chain 'E' and resid 23 through 53
    Processing helix  chain 'E' and resid 58 through 68
      removed outlier: 3.611A  pdb=" N   LYS E  68 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 6 through 18
    Processing helix  chain 'F' and resid 23 through 53
    Processing helix  chain 'F' and resid 58 through 66
    Processing helix  chain 'G' and resid 6 through 18
    Processing helix  chain 'G' and resid 23 through 53
    Processing helix  chain 'G' and resid 58 through 68
      removed outlier: 3.553A  pdb=" N   LYS G  68 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 6 through 17
    Processing helix  chain 'H' and resid 23 through 53
    Processing helix  chain 'H' and resid 58 through 67
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 7.115A  pdb=" N   ARG A  21 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57
    Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 22
      removed outlier: 7.278A  pdb=" N   ARG C  21 " --> pdb=" O   VAL D  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 57
    Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22
      removed outlier: 7.057A  pdb=" N   ARG E  21 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57
    Processing sheet with id=AA7, first strand: chain 'G' and resid 21 through 22
      removed outlier: 7.219A  pdb=" N   ARG G  21 " --> pdb=" O   VAL H  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57

    331 hydrogen bonds defined for protein.
    993 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      221 hydrogen bonds
      436 hydrogen bond angles
      0 basepair planarities
      90 basepair parallelities
      183 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.58 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: 1388
        1.33 -     1.45: 3201
        1.45 -     1.57: 4157
        1.57 -     1.69: 478
        1.69 -     1.81: 24
  Bond restraints: 9248
  Sorted by residual:
  bond pdb=" CA  SER C  23 "
       pdb=" CB  SER C  23 "
    ideal  model  delta    sigma   weight residual
    1.529  1.458  0.070 1.53e-02 4.27e+03 2.12e+01
  bond pdb=" CA  SER D  23 "
       pdb=" CB  SER D  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.467  0.063 1.48e-02 4.57e+03 1.79e+01
  bond pdb=" CA  SER A  23 "
       pdb=" CB  SER A  23 "
    ideal  model  delta    sigma   weight residual
    1.529  1.473  0.056 1.58e-02 4.01e+03 1.26e+01
  bond pdb=" CA  SER F  23 "
       pdb=" CB  SER F  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.475  0.055 1.55e-02 4.16e+03 1.25e+01
  bond pdb=" N   GLY A   3 "
       pdb=" CA  GLY A   3 "
    ideal  model  delta    sigma   weight residual
    1.444  1.476 -0.032 1.02e-02 9.61e+03 1.01e+01
  ... (remaining 9243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 10879
        2.21 -     4.42: 2018
        4.42 -     6.64: 501
        6.64 -     8.85: 49
        8.85 -    11.06: 3
  Bond angle restraints: 13450
  Sorted by residual:
  angle pdb=" O3'  DC X  67 "
        pdb=" P    DC X  68 "
        pdb=" O5'  DC X  68 "
      ideal   model   delta    sigma   weight residual
     104.00   92.94   11.06 1.50e+00 4.44e-01 5.44e+01
  angle pdb=" CA  ALA C  42 "
        pdb=" C   ALA C  42 "
        pdb=" O   ALA C  42 "
      ideal   model   delta    sigma   weight residual
     120.42  114.86    5.56 1.06e+00 8.90e-01 2.75e+01
  angle pdb=" N   LYS F  55 "
        pdb=" CA  LYS F  55 "
        pdb=" C   LYS F  55 "
      ideal   model   delta    sigma   weight residual
     113.28  107.00    6.28 1.22e+00 6.72e-01 2.65e+01
  angle pdb=" CA  ARG B  21 "
        pdb=" C   ARG B  21 "
        pdb=" O   ARG B  21 "
      ideal   model   delta    sigma   weight residual
     121.40  116.09    5.31 1.13e+00 7.83e-01 2.21e+01
  angle pdb=" N   GLY D  53 "
        pdb=" CA  GLY D  53 "
        pdb=" C   GLY D  53 "
      ideal   model   delta    sigma   weight residual
     114.69  109.14    5.55 1.19e+00 7.06e-01 2.18e+01
  ... (remaining 13445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 3697
       35.97 -    71.94: 977
       71.94 -   107.90: 26
      107.90 -   143.87: 0
      143.87 -   179.84: 18
  Dihedral angle restraints: 4718
    sinusoidal: 3408
      harmonic: 1310
  Sorted by residual:
  dihedral pdb=" CD  ARG B  21 "
           pdb=" NE  ARG B  21 "
           pdb=" CZ  ARG B  21 "
           pdb=" NH1 ARG B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.98  -84.98     1      1.00e+01 1.00e-02 8.76e+01
  dihedral pdb=" CD  ARG F  54 "
           pdb=" NE  ARG F  54 "
           pdb=" CZ  ARG F  54 "
           pdb=" NH1 ARG F  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.94  -81.94     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" CD  ARG B  50 "
           pdb=" NE  ARG B  50 "
           pdb=" CZ  ARG B  50 "
           pdb=" NH1 ARG B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.03  -80.03     1      1.00e+01 1.00e-02 7.94e+01
  ... (remaining 4715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1100
       0.131 -    0.261: 96
       0.261 -    0.392: 16
       0.392 -    0.523: 163
       0.523 -    0.653: 59
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" P    DC X  29 "
            pdb=" OP1  DC X  29 "
            pdb=" OP2  DC X  29 "
            pdb=" O5'  DC X  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.00   -0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" P    DC Y  20 "
            pdb=" OP1  DC Y  20 "
            pdb=" OP2  DC Y  20 "
            pdb=" O5'  DC Y  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.72e+00
  chirality pdb=" P    DG Y  83 "
            pdb=" OP1  DG Y  83 "
            pdb=" OP2  DG Y  83 "
            pdb=" O5'  DG Y  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.61e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  21 "   -1.109 9.50e-02 1.11e+02   4.97e-01 1.49e+02
        pdb=" NE  ARG B  21 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  21 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  21 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  21 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  54 "   -1.091 9.50e-02 1.11e+02   4.89e-01 1.44e+02
        pdb=" NE  ARG F  54 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  54 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  54 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  54 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  50 "   -1.058 9.50e-02 1.11e+02   4.74e-01 1.37e+02
        pdb=" NE  ARG B  50 "    0.069 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  50 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 931 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 2904
        2.92 -     3.42: 8499
        3.42 -     3.91: 16761
        3.91 -     4.41: 18856
        4.41 -     4.90: 25024
  Nonbonded interactions: 72044
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  47 "
            pdb=" NE2 HIS C  51 "
     model   vdw
     2.431 3.120
  nonbonded pdb=" O5'  DA Y  76 "
            pdb=" O4'  DA Y  76 "
     model   vdw
     2.493 2.432
  nonbonded pdb=" N   ALA F  66 "
            pdb=" O   ALA F  66 "
     model   vdw
     2.496 2.496
  nonbonded pdb=" O5'  DC X  40 "
            pdb=" O4'  DC X  40 "
     model   vdw
     2.499 2.432
  nonbonded pdb=" CA  SER H  23 "
            pdb=" OP1  DG Y 106 "
     model   vdw
     2.538 3.470
  ... (remaining 72039 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'B' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'C' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'D' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'E' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'F' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = chain 'G'
  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:             13.290
  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:             0.000
  Extract box with map and model:          1.010
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.690
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
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      :  0.013   0.070   9248  Z= 0.784
  Angle     :  1.872  11.061  13450  Z= 1.117
  Chirality :  0.209   0.653   1434
  Planarity :  0.043   0.497    934
  Dihedral  : 31.178 179.841   3950
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  1.60 %
    Favored  : 97.44 %
  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: -0.79 (0.30), residues: 528
  helix: -0.20 (0.22), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.24 (0.40), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  50 
 TYR   0.018   0.003   TYR C  44 
 PHE   0.021   0.006   PHE A   5 
 TRP   0.026   0.010   TRP C  37 
 HIS   0.004   0.002   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.01326 ( 9248)
  covalent geometry    : angle       1.87172 (13450)
  hydrogen bonds       : bond        0.21320 (  552)
  hydrogen bonds       : angle       8.50119 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.8242 (m-40) cc_final: 0.7910 (m-40)
REVERT: A   12 LYS cc_start: 0.9104 (tttt) cc_final: 0.8784 (tmmt)
REVERT: A   37 TRP cc_start: 0.7621 (t60) cc_final: 0.6716 (t60)
REVERT: B    4 ASN cc_start: 0.8634 (m110) cc_final: 0.7944 (m-40)
REVERT: B   11 GLU cc_start: 0.8885 (tt0) cc_final: 0.8530 (tt0)
REVERT: B   60 ASN cc_start: 0.8065 (m-40) cc_final: 0.7762 (t0)
REVERT: E   11 GLU cc_start: 0.8600 (tt0) cc_final: 0.7771 (tm-30)
REVERT: E   15 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8086 (mtt90)
REVERT: E   23 SER cc_start: 0.9262 (m) cc_final: 0.8917 (p)
REVERT: F   56 THR cc_start: 0.8121 (m) cc_final: 0.7734 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1275
  time to fit residues: 18.5041
Evaluate side-chains
  96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:   30.0000
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   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   4 ASN
D   4 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.156608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.095931 restraints weight = 18277.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.099266 restraints weight = 8698.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.101578 restraints weight = 5596.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.102981 restraints weight = 4321.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.103858 restraints weight = 3745.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054   9248  Z= 0.337
  Angle     :  0.780   6.247  13450  Z= 0.466
  Chirality :  0.047   0.200   1434
  Planarity :  0.005   0.061    934
  Dihedral  : 34.174 177.272   3170
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.82 %
    Favored  : 84.62 %
  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:  2.17 (0.33), residues: 528
  helix:  1.95 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.45 (0.48), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  54 
 TYR   0.012   0.002   TYR D  44 
 PHE   0.018   0.003   PHE D   5 
 TRP   0.013   0.003   TRP C  37 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 ( 9248)
  covalent geometry    : angle       0.78037 (13450)
  hydrogen bonds       : bond        0.06968 (  552)
  hydrogen bonds       : angle       3.87386 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.9049 (tttt) cc_final: 0.8714 (tmmt)
REVERT: A   20 GLN cc_start: 0.8781 (mp10) cc_final: 0.8272 (mp10)
REVERT: A   37 TRP cc_start: 0.7814 (t60) cc_final: 0.7491 (t60)
REVERT: B    4 ASN cc_start: 0.8676 (m110) cc_final: 0.7346 (t0)
REVERT: B   20 GLN cc_start: 0.8283 (pt0) cc_final: 0.8000 (tm-30)
REVERT: B   21 ARG cc_start: 0.8634 (mtp85) cc_final: 0.7694 (mtp85)
REVERT: B   37 TRP cc_start: 0.8322 (t60) cc_final: 0.7769 (t60)
REVERT: F   37 TRP cc_start: 0.7833 (t60) cc_final: 0.7421 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 103
  average time/residue: 0.1494
  time to fit residues: 19.1341
Evaluate side-chains
  97 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain F residue   23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:   50.0000
   chunk 55 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
C  51 HIS
D   4 ASN
F  20 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.160862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.098987 restraints weight = 18233.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.102295 restraints weight = 9052.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.104549 restraints weight = 5927.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.106043 restraints weight = 4659.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106848 restraints weight = 4077.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9248  Z= 0.205
  Angle     :  0.637   6.236  13450  Z= 0.385
  Chirality :  0.037   0.158   1434
  Planarity :  0.003   0.034    934
  Dihedral  : 33.560 177.650   3170
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.91 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.55 (0.34), residues: 528
  helix:  2.98 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.26 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F   9 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.013   0.002   PHE D   5 
 TRP   0.008   0.001   TRP A  37 
 HIS   0.001   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 9248)
  covalent geometry    : angle       0.63676 (13450)
  hydrogen bonds       : bond        0.05647 (  552)
  hydrogen bonds       : angle       3.17022 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8934 (tttt) cc_final: 0.8646 (tmmt)
REVERT: A   37 TRP cc_start: 0.7788 (t60) cc_final: 0.6973 (t60)
REVERT: A   54 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7274 (mtm180)
REVERT: B   21 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8065 (mtp85)
REVERT: E   23 SER cc_start: 0.9249 (m) cc_final: 0.8820 (p)
REVERT: F   37 TRP cc_start: 0.7738 (t60) cc_final: 0.7327 (t60)
REVERT: F   48 ILE cc_start: 0.8195 (tt) cc_final: 0.7912 (tt)
  outliers start: 7
  outliers final: 2
  residues processed: 95
  average time/residue: 0.1227
  time to fit residues: 14.4138
Evaluate side-chains
  86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain D residue   23 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  67 GLN
C  16 GLN
C  67 GLN
D   4 ASN
E  20 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.162727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.101311 restraints weight = 18708.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.104967 restraints weight = 8758.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.107457 restraints weight = 5564.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.108941 restraints weight = 4281.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.109883 restraints weight = 3720.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.5037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9248  Z= 0.157
  Angle     :  0.579   5.663  13450  Z= 0.350
  Chirality :  0.033   0.140   1434
  Planarity :  0.003   0.023    934
  Dihedral  : 33.254 179.500   3170
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.55 %
    Favored  : 77.24 %
  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:  4.44 (0.34), residues: 528
  helix:  3.66 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.27 (0.48), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  50 
 TYR   0.005   0.001   TYR D  44 
 PHE   0.007   0.002   PHE D   5 
 TRP   0.004   0.001   TRP D  37 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9248)
  covalent geometry    : angle       0.57857 (13450)
  hydrogen bonds       : bond        0.04918 (  552)
  hydrogen bonds       : angle       2.68213 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8831 (tttt) cc_final: 0.8576 (tmmt)
REVERT: A   37 TRP cc_start: 0.7721 (t60) cc_final: 0.7131 (t60)
REVERT: B    1 MET cc_start: 0.4154 (OUTLIER) cc_final: 0.3598 (mtt)
REVERT: B   36 ASP cc_start: 0.8835 (t0) cc_final: 0.8589 (t0)
REVERT: C   43 LYS cc_start: 0.8356 (tppt) cc_final: 0.7974 (ttmm)
REVERT: F   37 TRP cc_start: 0.7616 (t60) cc_final: 0.7255 (t60)
REVERT: F   48 ILE cc_start: 0.8042 (tt) cc_final: 0.7728 (tt)
  outliers start: 10
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1220
  time to fit residues: 13.9374
Evaluate side-chains
  85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASN
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   37 TRP
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain F residue   23 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:   50.0000
   chunk 45 optimal weight:   30.0000
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:   50.0000
   overall best weight:    2.7584

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
C  16 GLN
** E  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.158687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096334 restraints weight = 17955.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.099572 restraints weight = 8813.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.101732 restraints weight = 5789.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.102993 restraints weight = 4565.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.103813 restraints weight = 4025.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9248  Z= 0.222
  Angle     :  0.607   6.276  13450  Z= 0.362
  Chirality :  0.035   0.137   1434
  Planarity :  0.003   0.021    934
  Dihedral  : 33.262 178.475   3170
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.47 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.12 (0.34), residues: 528
  helix:  3.41 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.24 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  54 
 TYR   0.006   0.001   TYR B  44 
 PHE   0.012   0.002   PHE D   5 
 TRP   0.003   0.001   TRP A  37 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 9248)
  covalent geometry    : angle       0.60681 (13450)
  hydrogen bonds       : bond        0.05688 (  552)
  hydrogen bonds       : angle       3.15710 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5587 (mmm) cc_final: 0.5303 (mmm)
REVERT: A   12 LYS cc_start: 0.8926 (tttt) cc_final: 0.8645 (tmmt)
REVERT: A   37 TRP cc_start: 0.7874 (t60) cc_final: 0.7046 (t60)
REVERT: B    1 MET cc_start: 0.4340 (mtt) cc_final: 0.3945 (mtt)
REVERT: B   21 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8100 (mtp85)
REVERT: B   30 MET cc_start: 0.8445 (tpt) cc_final: 0.8039 (tpt)
REVERT: B   36 ASP cc_start: 0.8808 (t0) cc_final: 0.8592 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1371
  time to fit residues: 14.8516
Evaluate side-chains
  87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   23 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 46 optimal weight:   30.0000
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 5 optimal weight:   30.0000
   chunk 67 optimal weight:    7.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
C  16 GLN
C  51 HIS
C  67 GLN
** E  20 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.155518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.092145 restraints weight = 18335.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095352 restraints weight = 9036.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097487 restraints weight = 5975.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.098961 restraints weight = 4719.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.099692 restraints weight = 4134.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.5371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   9248  Z= 0.317
  Angle     :  0.666   6.124  13450  Z= 0.396
  Chirality :  0.039   0.159   1434
  Planarity :  0.004   0.043    934
  Dihedral  : 33.542 177.124   3170
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.15 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.36 (0.34), residues: 528
  helix:  2.86 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG D  54 
 TYR   0.010   0.002   TYR A  44 
 PHE   0.013   0.003   PHE A   5 
 TRP   0.004   0.001   TRP C  37 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 9248)
  covalent geometry    : angle       0.66638 (13450)
  hydrogen bonds       : bond        0.06662 (  552)
  hydrogen bonds       : angle       3.60637 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.9013 (tttt) cc_final: 0.8673 (tmmt)
REVERT: A   37 TRP cc_start: 0.7911 (t60) cc_final: 0.6983 (t60)
REVERT: B    1 MET cc_start: 0.4531 (mtt) cc_final: 0.4226 (mtt)
REVERT: B    4 ASN cc_start: 0.8750 (m110) cc_final: 0.7406 (t0)
REVERT: B   36 ASP cc_start: 0.8854 (t0) cc_final: 0.8638 (t0)
REVERT: C   43 LYS cc_start: 0.8363 (tppt) cc_final: 0.7979 (ttmm)
REVERT: E   20 GLN cc_start: 0.8730 (pt0) cc_final: 0.8448 (pm20)
  outliers start: 12
  outliers final: 10
  residues processed: 89
  average time/residue: 0.1383
  time to fit residues: 15.4323
Evaluate side-chains
  91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   41 ILE
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   23 SER
Chi-restraints excluded: chain F residue   41 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:   50.0000
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:   50.0000
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  20 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 = 0.4439 r_free = 0.4439 target = 0.163760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.102059 restraints weight = 18500.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.105225 restraints weight = 9132.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.107584 restraints weight = 5992.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.109119 restraints weight = 4683.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.109967 restraints weight = 4092.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9248  Z= 0.160
  Angle     :  0.571   5.600  13450  Z= 0.343
  Chirality :  0.032   0.133   1434
  Planarity :  0.003   0.043    934
  Dihedral  : 33.101 178.924   3170
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 24.68 %
    Favored  : 74.36 %
  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:  4.40 (0.34), residues: 528
  helix:  3.67 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.42 (0.48), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  54 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.008   0.002   PHE D   5 
 TRP   0.007   0.001   TRP F  37 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9248)
  covalent geometry    : angle       0.57124 (13450)
  hydrogen bonds       : bond        0.05143 (  552)
  hydrogen bonds       : angle       2.69437 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8870 (tttt) cc_final: 0.8593 (tmmt)
REVERT: A   37 TRP cc_start: 0.7804 (t60) cc_final: 0.7015 (t60)
REVERT: B    1 MET cc_start: 0.4499 (mtt) cc_final: 0.4198 (mtt)
REVERT: B   11 GLU cc_start: 0.8906 (tt0) cc_final: 0.7930 (tm-30)
REVERT: B   36 ASP cc_start: 0.8815 (t0) cc_final: 0.8589 (t0)
REVERT: D   28 ASP cc_start: 0.8502 (t70) cc_final: 0.8040 (m-30)
REVERT: F   37 TRP cc_start: 0.7681 (t60) cc_final: 0.7205 (t60)
REVERT: F   50 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7431 (ptp-170)
  outliers start: 3
  outliers final: 2
  residues processed: 87
  average time/residue: 0.1400
  time to fit residues: 15.2225
Evaluate side-chains
  84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain F residue   27 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 70 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.158957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.095986 restraints weight = 18374.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098967 restraints weight = 9428.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.101167 restraints weight = 6293.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102471 restraints weight = 4988.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.103382 restraints weight = 4392.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9248  Z= 0.267
  Angle     :  0.625   5.078  13450  Z= 0.371
  Chirality :  0.036   0.149   1434
  Planarity :  0.003   0.034    934
  Dihedral  : 33.313 178.637   3170
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 23.08 %
    Favored  : 74.36 %
  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:  3.95 (0.34), residues: 528
  helix:  3.32 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.42 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  54 
 TYR   0.007   0.001   TYR B  44 
 PHE   0.012   0.003   PHE D   5 
 TRP   0.003   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 ( 9248)
  covalent geometry    : angle       0.62504 (13450)
  hydrogen bonds       : bond        0.06072 (  552)
  hydrogen bonds       : angle       3.28412 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8982 (tttt) cc_final: 0.8718 (tmmt)
REVERT: A   37 TRP cc_start: 0.7958 (t60) cc_final: 0.7077 (t60)
REVERT: B    4 ASN cc_start: 0.8673 (m110) cc_final: 0.7404 (t0)
REVERT: C   43 LYS cc_start: 0.8484 (tppt) cc_final: 0.8062 (ttmm)
REVERT: F   50 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7543 (ptp-170)
  outliers start: 8
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1184
  time to fit residues: 13.7211
Evaluate side-chains
  92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   23 SER
Chi-restraints excluded: chain F residue   27 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 60 optimal weight:   30.0000
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** B  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.163086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.101184 restraints weight = 18458.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.104429 restraints weight = 9198.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.106785 restraints weight = 6059.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.108202 restraints weight = 4763.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.108958 restraints weight = 4173.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.5886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9248  Z= 0.168
  Angle     :  0.571   5.449  13450  Z= 0.342
  Chirality :  0.032   0.130   1434
  Planarity :  0.003   0.030    934
  Dihedral  : 33.070 178.835   3170
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.76 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.50 (0.34), residues: 528
  helix:  3.75 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.45 (0.48), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  54 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.009   0.002   PHE D   5 
 TRP   0.006   0.001   TRP F  37 
 HIS   0.002   0.000   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 9248)
  covalent geometry    : angle       0.57110 (13450)
  hydrogen bonds       : bond        0.05243 (  552)
  hydrogen bonds       : angle       2.75467 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8916 (tttt) cc_final: 0.8614 (tmmt)
REVERT: A   37 TRP cc_start: 0.7841 (t60) cc_final: 0.6971 (t60)
REVERT: C   43 LYS cc_start: 0.8391 (tppt) cc_final: 0.7967 (ttmm)
REVERT: F   37 TRP cc_start: 0.7710 (t60) cc_final: 0.7212 (t60)
REVERT: F   50 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7451 (ptp-170)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1332
  time to fit residues: 14.5895
Evaluate side-chains
  88 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   23 SER
Chi-restraints excluded: chain F residue   27 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 70 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  51 HIS
C  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.158951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.099736 restraints weight = 18075.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.102838 restraints weight = 8680.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.104961 restraints weight = 5663.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.106322 restraints weight = 4446.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.107084 restraints weight = 3897.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.5917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9248  Z= 0.195
  Angle     :  0.585   7.182  13450  Z= 0.349
  Chirality :  0.032   0.140   1434
  Planarity :  0.003   0.030    934
  Dihedral  : 33.092 178.601   3170
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.76 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.45 (0.34), residues: 528
  helix:  3.71 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.43 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  54 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.008   0.002   PHE D   5 
 TRP   0.005   0.001   TRP F  37 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 9248)
  covalent geometry    : angle       0.58541 (13450)
  hydrogen bonds       : bond        0.05447 (  552)
  hydrogen bonds       : angle       2.88660 ( 1429)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8915 (tttt) cc_final: 0.8632 (tmmt)
REVERT: A   37 TRP cc_start: 0.7862 (t60) cc_final: 0.6929 (t60)
REVERT: C   43 LYS cc_start: 0.8374 (tppt) cc_final: 0.7947 (ttmm)
REVERT: F   50 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7449 (ptp-170)
  outliers start: 7
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1369
  time to fit residues: 14.8248
Evaluate side-chains
  89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASN
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   23 SER
Chi-restraints excluded: chain F residue   27 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 38 optimal weight:   40.0000
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 50 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 60 optimal weight:   30.0000
   chunk 54 optimal weight:    6.9990
   overall best weight:    3.0784

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

Flipped N/Q/H residues before XYZ refinement:
C  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.157311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095222 restraints weight = 17940.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098334 restraints weight = 8782.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.100480 restraints weight = 5815.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.101725 restraints weight = 4588.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.102516 restraints weight = 4045.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.5932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9248  Z= 0.238
  Angle     :  0.609   6.845  13450  Z= 0.360
  Chirality :  0.034   0.142   1434
  Planarity :  0.003   0.032    934
  Dihedral  : 33.213 179.417   3170
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.79 %
    Favored  : 75.32 %
  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:  4.19 (0.34), residues: 528
  helix:  3.51 (0.23), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.46 (0.50), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  54 
 TYR   0.007   0.001   TYR B  44 
 PHE   0.010   0.002   PHE D   5 
 TRP   0.004   0.001   TRP F  37 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 9248)
  covalent geometry    : angle       0.60873 (13450)
  hydrogen bonds       : bond        0.05884 (  552)
  hydrogen bonds       : angle       3.15978 ( 1429)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2325.20 seconds
wall clock time: 40 minutes 22.55 seconds (2422.55 seconds total)