Starting phenix.real_space_refine
on Fri Jul  3 14:01:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pff_13374/07_2026/7pff_13374.map"
  }
  resolution = 4.3
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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     334      5.49       5
     S      10      5.16       5
     C    7085      2.51       5
     N    2430      2.21       5
     O    3076      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12935
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "K"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "L"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "M"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "N"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "O"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "P"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "Q"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "R"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3407
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "J"
      Number of atoms: 3440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3440
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 2.24, per 1000 atoms: 0.17
  Number of scatterers: 12935
  At special positions: 0
  Unit cell: (128.1, 130.2, 112.35, 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      10     16.00
     P     334     15.00
     O    3076      8.00
     N    2430      7.00
     C    7085      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: 1.08
  Conformation dependent library (CDL) restraints added in 430.8 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      70.7% alpha, 2.6% beta
      167 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.741A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE K  78 " --> pdb=" O   ILE K  74 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.774A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.907A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 93
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.399A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 88
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 37 through 49
    Processing helix  chain 'N' and resid 55 through 84
    Processing helix  chain 'N' and resid 90 through 102
    Processing helix  chain 'N' and resid 104 through 123
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 76
      removed outlier: 3.579A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.994A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 29
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 4.060A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.765A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 16 through 22
    Processing helix  chain 'Q' and resid 26 through 37
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.173A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
      removed outlier: 3.536A  pdb=" N   ASN Q  89 " --> pdb=" O   LEU Q  85 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 90 through 97
    Processing helix  chain 'Q' and resid 112 through 116
    Processing helix  chain 'R' and resid 37 through 49
    Processing helix  chain 'R' and resid 55 through 84
    Processing helix  chain 'R' and resid 90 through 102
    Processing helix  chain 'R' and resid 104 through 124
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.933A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.321A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 102
      removed outlier: 6.465A  pdb=" N   THR M 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.779A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.350A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    401 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      427 hydrogen bonds
      854 hydrogen bond angles
      0 basepair planarities
      167 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 1.50 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: 2762
        1.33 -     1.46: 4906
        1.46 -     1.58: 5494
        1.58 -     1.70: 666
        1.70 -     1.83: 20
  Bond restraints: 13848
  Sorted by residual:
  bond pdb=" C5'  DA I 478 "
       pdb=" C4'  DA I 478 "
    ideal  model  delta    sigma   weight residual
    1.512  1.543 -0.031 7.00e-03 2.04e+04 1.99e+01
  bond pdb=" C3'  DA I 449 "
       pdb=" O3'  DA I 449 "
    ideal  model  delta    sigma   weight residual
    1.435  1.380  0.055 1.30e-02 5.92e+03 1.80e+01
  bond pdb=" O3'  DC I 563 "
       pdb=" P    DT I 564 "
    ideal  model  delta    sigma   weight residual
    1.607  1.665 -0.058 1.50e-02 4.44e+03 1.47e+01
  bond pdb=" C3'  DA J 302 "
       pdb=" C2'  DA J 302 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.27e+01
  bond pdb=" C5'  DC I 549 "
       pdb=" C4'  DC I 549 "
    ideal  model  delta    sigma   weight residual
    1.512  1.537 -0.025 7.00e-03 2.04e+04 1.27e+01
  ... (remaining 13843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 19092
        2.23 -     4.47: 953
        4.47 -     6.70: 71
        6.70 -     8.93: 16
        8.93 -    11.17: 3
  Bond angle restraints: 20135
  Sorted by residual:
  angle pdb=" O4'  DG I 519 "
        pdb=" C4'  DG I 519 "
        pdb=" C3'  DG I 519 "
      ideal   model   delta    sigma   weight residual
     106.00  102.17    3.83 6.00e-01 2.78e+00 4.08e+01
  angle pdb=" O4'  DA J 228 "
        pdb=" C4'  DA J 228 "
        pdb=" C3'  DA J 228 "
      ideal   model   delta    sigma   weight residual
     106.00  102.31    3.69 6.00e-01 2.78e+00 3.77e+01
  angle pdb=" O4'  DA I 458 "
        pdb=" C4'  DA I 458 "
        pdb=" C3'  DA I 458 "
      ideal   model   delta    sigma   weight residual
     106.00  102.52    3.48 6.00e-01 2.78e+00 3.37e+01
  angle pdb=" O5'  DA I 439 "
        pdb=" C5'  DA I 439 "
        pdb=" C4'  DA I 439 "
      ideal   model   delta    sigma   weight residual
     109.40  113.99   -4.59 8.00e-01 1.56e+00 3.29e+01
  angle pdb=" O4'  DC J 294 "
        pdb=" C1'  DC J 294 "
        pdb=" N1   DC J 294 "
      ideal   model   delta    sigma   weight residual
     108.00  111.99   -3.99 7.00e-01 2.04e+00 3.24e+01
  ... (remaining 20130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.49: 5567
       34.49 -    68.98: 1838
       68.98 -   103.47: 55
      103.47 -   137.96: 3
      137.96 -   172.46: 1
  Dihedral angle restraints: 7464
    sinusoidal: 5242
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  PRO R 103 "
           pdb=" C   PRO R 103 "
           pdb=" N   GLY R 104 "
           pdb=" CA  GLY R 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.31   20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ILE L  50 "
           pdb=" C   ILE L  50 "
           pdb=" N   TYR L  51 "
           pdb=" CA  TYR L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.09  -19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" C4'  DG J 316 "
           pdb=" C3'  DG J 316 "
           pdb=" O3'  DG J 316 "
           pdb=" P    DG J 317 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.54  172.46     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1897
       0.067 -    0.135: 354
       0.135 -    0.202: 32
       0.202 -    0.269: 4
       0.269 -    0.337: 1
  Chirality restraints: 2288
  Sorted by residual:
  chirality pdb=" C3'  DC I 562 "
            pdb=" C4'  DC I 562 "
            pdb=" O3'  DC I 562 "
            pdb=" C2'  DC I 562 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.39   -0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" C3'  DC J 238 "
            pdb=" C4'  DC J 238 "
            pdb=" O3'  DC J 238 "
            pdb=" C2'  DC J 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.50   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C4'  DA I 439 "
            pdb=" C5'  DA I 439 "
            pdb=" O4'  DA I 439 "
            pdb=" C3'  DA I 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.32   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 2285 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU R 113 "    0.019 2.00e-02 2.50e+03   3.89e-02 1.51e+01
        pdb=" CD  GLU R 113 "   -0.067 2.00e-02 2.50e+03
        pdb=" OE1 GLU R 113 "    0.024 2.00e-02 2.50e+03
        pdb=" OE2 GLU R 113 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I 560 "    0.047 2.00e-02 2.50e+03   2.08e-02 1.19e+01
        pdb=" N9   DA I 560 "   -0.045 2.00e-02 2.50e+03
        pdb=" C8   DA I 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I 560 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DA I 560 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I 560 "    0.016 2.00e-02 2.50e+03
        pdb=" N1   DA I 560 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I 560 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DA I 560 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I 560 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K 104 "    0.013 2.00e-02 2.50e+03   2.00e-02 7.00e+00
        pdb=" CG  PHE K 104 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE K 104 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE K 104 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE K 104 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE K 104 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE K 104 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3108
        2.81 -     3.33: 12445
        3.33 -     3.85: 28738
        3.85 -     4.38: 31734
        4.38 -     4.90: 43238
  Nonbonded interactions: 119263
  Sorted by model distance:
  nonbonded pdb=" O   VAL N 118 "
            pdb=" OG1 THR N 122 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   THR Q  16 "
            pdb=" OG  SER Q  19 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASP K 123 "
            pdb=" NE2 HIS O 113 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   GLN K  55 "
            pdb=" NH2 ARG Q  81 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH2 ARG M  81 "
            pdb=" O   GLN O  55 "
     model   vdw
     2.311 3.120
  ... (remaining 119258 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 'K'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'R'
}

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:             2.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.190
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  13848  Z= 0.644
  Angle     :  1.049  11.167  20135  Z= 0.857
  Chirality :  0.052   0.337   2288
  Planarity :  0.007   0.071   1390
  Dihedral  : 30.348 172.456   6032
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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: -0.07 (0.28), residues: 752
  helix:  0.19 (0.21), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.28 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P  95 
 TYR   0.033   0.003   TYR O  54 
 PHE   0.045   0.004   PHE K 104 
 HIS   0.009   0.002   HIS N 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00717 /  0.64 (13848)
  covalent geometry    : angle       1.04912 /  0.86 (20135)
  hydrogen bonds       : bond        0.11994 /  7.97 (  828)
  hydrogen bonds       : angle       4.62731 /  3.38 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9229 (m-80) cc_final: 0.8907 (m-80)
REVERT: N  109 HIS cc_start: 0.9687 (m-70) cc_final: 0.9380 (m90)
REVERT: O   81 ASP cc_start: 0.9446 (m-30) cc_final: 0.9066 (p0)
REVERT: R  102 LEU cc_start: 0.8679 (tp) cc_final: 0.8386 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0865
  time to fit residues: 12.0169
Evaluate side-chains
  62 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N 109 HIS
O  76 GLN
P  25 ASN
R 109 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.037588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.031363 restraints weight = 193529.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.032312 restraints weight = 112275.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.032925 restraints weight = 75150.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.033402 restraints weight = 55592.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.033771 restraints weight = 43040.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13848  Z= 0.181
  Angle     :  0.770   9.783  20135  Z= 0.450
  Chirality :  0.054   0.344   2288
  Planarity :  0.006   0.066   1390
  Dihedral  : 33.956 178.857   4508
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.26 %
    Favored  : 98.58 %
  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:  0.61 (0.29), residues: 752
  helix:  0.74 (0.21), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  95 
 TYR   0.018   0.002   TYR O  54 
 PHE   0.012   0.002   PHE O 104 
 HIS   0.008   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.18 (13848)
  covalent geometry    : angle       0.76964 /  0.45 (20135)
  hydrogen bonds       : bond        0.06822 /  4.75 (  828)
  hydrogen bonds       : angle       3.87272 /  2.76 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9480 (m-80) cc_final: 0.9046 (m-80)
REVERT: K  104 PHE cc_start: 0.9717 (m-10) cc_final: 0.9454 (m-80)
REVERT: K  105 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9460 (mt-10)
REVERT: N  109 HIS cc_start: 0.9455 (m90) cc_final: 0.9118 (m90)
REVERT: O   54 TYR cc_start: 0.9044 (m-80) cc_final: 0.8748 (m-80)
REVERT: O  104 PHE cc_start: 0.9461 (m-80) cc_final: 0.9234 (m-80)
REVERT: Q   26 PRO cc_start: 0.7313 (Cg_endo) cc_final: 0.7028 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9033 (tp) cc_final: 0.8697 (tp)
REVERT: R  109 HIS cc_start: 0.9531 (m90) cc_final: 0.9021 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0947
  time to fit residues: 11.6354
Evaluate side-chains
  58 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 97 optimal weight:   30.0000
   chunk 9 optimal weight:    0.0060
   chunk 81 optimal weight:   30.0000
   overall best weight:    3.1802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M  84 GLN
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.035662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.028636 restraints weight = 178218.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.029540 restraints weight = 107661.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.030153 restraints weight = 75254.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.030593 restraints weight = 57475.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.030911 restraints weight = 46635.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  13848  Z= 0.189
  Angle     :  0.736   9.248  20135  Z= 0.433
  Chirality :  0.051   0.299   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 33.913 174.478   4508
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.04 %
    Favored  : 97.64 %
  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:  0.99 (0.29), residues: 752
  helix:  1.04 (0.21), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.10 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  95 
 TYR   0.016   0.002   TYR Q  57 
 PHE   0.011   0.002   PHE N  65 
 HIS   0.004   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.19 (13848)
  covalent geometry    : angle       0.73587 /  0.43 (20135)
  hydrogen bonds       : bond        0.07948 /  5.47 (  828)
  hydrogen bonds       : angle       3.80091 /  2.69 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9467 (m-80) cc_final: 0.9060 (m-80)
REVERT: K  100 LEU cc_start: 0.9913 (mt) cc_final: 0.9659 (mp)
REVERT: K  104 PHE cc_start: 0.9717 (m-10) cc_final: 0.9496 (m-80)
REVERT: K  105 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9458 (mt-10)
REVERT: N  108 LYS cc_start: 0.9664 (ptpp) cc_final: 0.9415 (ptpt)
REVERT: N  109 HIS cc_start: 0.9395 (m90) cc_final: 0.9015 (m90)
REVERT: O   54 TYR cc_start: 0.9003 (m-80) cc_final: 0.8750 (m-80)
REVERT: O  104 PHE cc_start: 0.9445 (m-80) cc_final: 0.9223 (m-80)
REVERT: Q   26 PRO cc_start: 0.7186 (Cg_endo) cc_final: 0.6893 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9133 (tp) cc_final: 0.8799 (tp)
REVERT: R  105 GLU cc_start: 0.9624 (tp30) cc_final: 0.9416 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 78
  average time/residue: 0.0873
  time to fit residues: 10.5009
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 99 optimal weight:   30.0000
   chunk 73 optimal weight:   30.0000
   chunk 4 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 87 optimal weight:   30.0000
   chunk 45 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.043941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.031853 restraints weight = 138230.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.033157 restraints weight = 89851.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.034127 restraints weight = 66748.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.034851 restraints weight = 53361.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.035426 restraints weight = 44860.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13848  Z= 0.168
  Angle     :  0.702   9.946  20135  Z= 0.413
  Chirality :  0.049   0.289   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 33.948 174.562   4508
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  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:  1.15 (0.29), residues: 752
  helix:  1.16 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  35 
 TYR   0.022   0.002   TYR L  51 
 PHE   0.010   0.001   PHE R  70 
 HIS   0.005   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.17 (13848)
  covalent geometry    : angle       0.70223 /  0.41 (20135)
  hydrogen bonds       : bond        0.06363 /  4.40 (  828)
  hydrogen bonds       : angle       3.68307 /  2.61 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   26 PRO cc_start: 0.7881 (Cg_endo) cc_final: 0.7662 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0928
  time to fit residues: 11.4998
Evaluate side-chains
  53 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
O 108 ASN
R  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.037416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.031250 restraints weight = 194668.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.032205 restraints weight = 110660.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.032852 restraints weight = 73369.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.033345 restraints weight = 53349.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.033674 restraints weight = 41577.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13848  Z= 0.154
  Angle     :  0.693   9.677  20135  Z= 0.408
  Chirality :  0.049   0.291   2288
  Planarity :  0.004   0.061   1390
  Dihedral  : 33.872 173.313   4508
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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:  1.20 (0.29), residues: 752
  helix:  1.20 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  95 
 TYR   0.018   0.001   TYR Q  57 
 PHE   0.042   0.002   PHE K 104 
 HIS   0.003   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.15 (13848)
  covalent geometry    : angle       0.69344 /  0.41 (20135)
  hydrogen bonds       : bond        0.05681 /  3.93 (  828)
  hydrogen bonds       : angle       3.67003 /  2.60 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9436 (m-80) cc_final: 0.8966 (m-80)
REVERT: K  104 PHE cc_start: 0.9585 (m-80) cc_final: 0.9298 (m-80)
REVERT: K  108 ASN cc_start: 0.9017 (t0) cc_final: 0.8201 (p0)
REVERT: N  108 LYS cc_start: 0.9661 (ptpp) cc_final: 0.9429 (ptpt)
REVERT: N  109 HIS cc_start: 0.9435 (m90) cc_final: 0.9107 (m90)
REVERT: O   54 TYR cc_start: 0.9243 (m-80) cc_final: 0.8997 (m-80)
REVERT: Q   26 PRO cc_start: 0.6383 (Cg_endo) cc_final: 0.5941 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8971 (tp) cc_final: 0.8713 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1013
  time to fit residues: 12.6157
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 97 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:   40.0000
   chunk 46 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.036940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.030796 restraints weight = 196540.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.031703 restraints weight = 114397.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.032307 restraints weight = 76951.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.032779 restraints weight = 57257.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.033134 restraints weight = 44632.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13848  Z= 0.169
  Angle     :  0.698  10.184  20135  Z= 0.410
  Chirality :  0.048   0.278   2288
  Planarity :  0.005   0.061   1390
  Dihedral  : 33.847 172.676   4508
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  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:  1.32 (0.30), residues: 752
  helix:  1.31 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.13 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.016   0.002   TYR N  42 
 PHE   0.028   0.002   PHE K 104 
 HIS   0.012   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.17 (13848)
  covalent geometry    : angle       0.69827 /  0.41 (20135)
  hydrogen bonds       : bond        0.06776 /  4.66 (  828)
  hydrogen bonds       : angle       3.66404 /  2.59 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9437 (m-80) cc_final: 0.9041 (m-80)
REVERT: K  104 PHE cc_start: 0.9595 (m-80) cc_final: 0.9288 (m-80)
REVERT: K  108 ASN cc_start: 0.9092 (t0) cc_final: 0.8306 (p0)
REVERT: N  108 LYS cc_start: 0.9653 (ptpp) cc_final: 0.9415 (ptpp)
REVERT: N  109 HIS cc_start: 0.9430 (m90) cc_final: 0.9070 (m90)
REVERT: O   54 TYR cc_start: 0.9241 (m-80) cc_final: 0.8999 (m-80)
REVERT: Q   26 PRO cc_start: 0.6466 (Cg_endo) cc_final: 0.6027 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8986 (tp) cc_final: 0.8718 (tp)
REVERT: R  105 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: R  109 HIS cc_start: 0.9611 (m90) cc_final: 0.9190 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0927
  time to fit residues: 11.1489
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 83 optimal weight:   30.0000
   chunk 21 optimal weight:   10.0000
   chunk 80 optimal weight:   30.0000
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 84 optimal weight:   30.0000
   chunk 52 optimal weight:    2.9990
   chunk 76 optimal weight:   30.0000
   chunk 41 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.035588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.029572 restraints weight = 205258.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.030456 restraints weight = 118454.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.031047 restraints weight = 79655.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.031502 restraints weight = 58619.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.031853 restraints weight = 45779.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13848  Z= 0.202
  Angle     :  0.732  11.371  20135  Z= 0.425
  Chirality :  0.049   0.280   2288
  Planarity :  0.005   0.062   1390
  Dihedral  : 33.989 171.640   4508
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.10 (0.30), residues: 752
  helix:  1.20 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.34 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  95 
 TYR   0.014   0.002   TYR L  51 
 PHE   0.018   0.002   PHE K 104 
 HIS   0.005   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.20 (13848)
  covalent geometry    : angle       0.73194 /  0.43 (20135)
  hydrogen bonds       : bond        0.09033 /  6.16 (  828)
  hydrogen bonds       : angle       3.86148 /  2.74 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9419 (m-80) cc_final: 0.9059 (m-80)
REVERT: K  104 PHE cc_start: 0.9672 (m-80) cc_final: 0.9405 (m-80)
REVERT: K  108 ASN cc_start: 0.9175 (t0) cc_final: 0.8404 (p0)
REVERT: N  109 HIS cc_start: 0.9471 (m90) cc_final: 0.9060 (m90)
REVERT: O   54 TYR cc_start: 0.9257 (m-80) cc_final: 0.9023 (m-80)
REVERT: Q   26 PRO cc_start: 0.6529 (Cg_endo) cc_final: 0.6104 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9049 (tp) cc_final: 0.8697 (tp)
REVERT: R  106 LEU cc_start: 0.9152 (mt) cc_final: 0.8936 (mt)
REVERT: R  109 HIS cc_start: 0.9620 (m90) cc_final: 0.9155 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1051
  time to fit residues: 12.6614
Evaluate side-chains
  59 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 88 optimal weight:   40.0000
   chunk 53 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0040
   chunk 74 optimal weight:   40.0000
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.037482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.031354 restraints weight = 192690.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.032274 restraints weight = 110812.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.032900 restraints weight = 74440.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.033400 restraints weight = 55004.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.033764 restraints weight = 42413.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  13848  Z= 0.150
  Angle     :  0.686  10.017  20135  Z= 0.404
  Chirality :  0.048   0.274   2288
  Planarity :  0.004   0.058   1390
  Dihedral  : 33.882 171.618   4508
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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:  1.19 (0.30), residues: 752
  helix:  1.25 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.28 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O 116 
 TYR   0.008   0.001   TYR O  54 
 PHE   0.030   0.002   PHE O 104 
 HIS   0.012   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.15 (13848)
  covalent geometry    : angle       0.68635 /  0.40 (20135)
  hydrogen bonds       : bond        0.04926 /  3.39 (  828)
  hydrogen bonds       : angle       3.63754 /  2.57 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9348 (m-80) cc_final: 0.8986 (m-80)
REVERT: K  104 PHE cc_start: 0.9650 (m-80) cc_final: 0.9409 (m-80)
REVERT: N  109 HIS cc_start: 0.9471 (m90) cc_final: 0.9118 (m-70)
REVERT: O   54 TYR cc_start: 0.9179 (m-80) cc_final: 0.8906 (m-80)
REVERT: O   81 ASP cc_start: 0.9270 (m-30) cc_final: 0.8952 (p0)
REVERT: Q   26 PRO cc_start: 0.6383 (Cg_endo) cc_final: 0.5928 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8941 (tp) cc_final: 0.8670 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0999
  time to fit residues: 13.2283
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 15 optimal weight:    0.3980
   chunk 17 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 103 optimal weight:   30.0000
   overall best weight:    2.0788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.036731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.030650 restraints weight = 198385.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.031568 restraints weight = 114690.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.032201 restraints weight = 76590.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.032671 restraints weight = 56090.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.033027 restraints weight = 43460.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13848  Z= 0.159
  Angle     :  0.692  10.371  20135  Z= 0.404
  Chirality :  0.047   0.264   2288
  Planarity :  0.004   0.059   1390
  Dihedral  : 33.787 170.581   4508
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.29 (0.30), residues: 752
  helix:  1.36 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.36 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  95 
 TYR   0.011   0.001   TYR L  51 
 PHE   0.017   0.001   PHE K 104 
 HIS   0.003   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.16 (13848)
  covalent geometry    : angle       0.69217 /  0.40 (20135)
  hydrogen bonds       : bond        0.06310 /  4.33 (  828)
  hydrogen bonds       : angle       3.62077 /  2.54 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9444 (mt) cc_final: 0.9227 (mm)
REVERT: K   54 TYR cc_start: 0.9386 (m-80) cc_final: 0.9005 (m-80)
REVERT: K  104 PHE cc_start: 0.9623 (m-80) cc_final: 0.9360 (m-80)
REVERT: N  108 LYS cc_start: 0.9654 (ptpp) cc_final: 0.9400 (ptpp)
REVERT: N  109 HIS cc_start: 0.9464 (m90) cc_final: 0.9085 (m90)
REVERT: O   54 TYR cc_start: 0.9214 (m-80) cc_final: 0.8933 (m-80)
REVERT: Q   26 PRO cc_start: 0.6407 (Cg_endo) cc_final: 0.5959 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8915 (tp) cc_final: 0.8636 (tp)
REVERT: R  105 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: R  109 HIS cc_start: 0.9635 (m90) cc_final: 0.9181 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0998
  time to fit residues: 12.0551
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 93 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 96 optimal weight:   30.0000
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.036983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.030938 restraints weight = 195882.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.031843 restraints weight = 113099.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.032489 restraints weight = 75421.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.032960 restraints weight = 54976.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.033307 restraints weight = 42469.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13848  Z= 0.152
  Angle     :  0.679  10.578  20135  Z= 0.398
  Chirality :  0.047   0.276   2288
  Planarity :  0.004   0.056   1390
  Dihedral  : 33.766 168.017   4508
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  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:  1.32 (0.30), residues: 752
  helix:  1.38 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.35 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.011   0.001   TYR Q  57 
 PHE   0.018   0.001   PHE K 104 
 HIS   0.003   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.15 (13848)
  covalent geometry    : angle       0.67928 /  0.40 (20135)
  hydrogen bonds       : bond        0.05158 /  3.53 (  828)
  hydrogen bonds       : angle       3.56686 /  2.50 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9396 (mt) cc_final: 0.9192 (mm)
REVERT: K   54 TYR cc_start: 0.9377 (m-80) cc_final: 0.9016 (m-80)
REVERT: K   94 GLU cc_start: 0.8904 (tp30) cc_final: 0.8661 (tp30)
REVERT: K  104 PHE cc_start: 0.9609 (m-80) cc_final: 0.9336 (m-80)
REVERT: N  108 LYS cc_start: 0.9646 (ptpp) cc_final: 0.9403 (ptpp)
REVERT: N  109 HIS cc_start: 0.9455 (m90) cc_final: 0.9084 (m-70)
REVERT: O   54 TYR cc_start: 0.9214 (m-80) cc_final: 0.8927 (m-80)
REVERT: Q   26 PRO cc_start: 0.6457 (Cg_endo) cc_final: 0.6009 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8826 (tp) cc_final: 0.8538 (tp)
REVERT: R  105 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8575 (tm-30)
REVERT: R  109 HIS cc_start: 0.9631 (m90) cc_final: 0.9180 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0989
  time to fit residues: 12.3921
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:   30.0000
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 74 optimal weight:   40.0000
   chunk 8 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.036320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.030381 restraints weight = 198067.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.031268 restraints weight = 114854.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.031901 restraints weight = 76435.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.032337 restraints weight = 55709.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.032670 restraints weight = 43447.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13848  Z= 0.166
  Angle     :  0.689  10.796  20135  Z= 0.402
  Chirality :  0.047   0.269   2288
  Planarity :  0.005   0.052   1390
  Dihedral  : 33.727 167.495   4508
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.33 (0.30), residues: 752
  helix:  1.39 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.35 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG O 116 
 TYR   0.009   0.001   TYR L  51 
 PHE   0.018   0.001   PHE K 104 
 HIS   0.003   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.17 (13848)
  covalent geometry    : angle       0.68941 /  0.40 (20135)
  hydrogen bonds       : bond        0.06725 /  4.59 (  828)
  hydrogen bonds       : angle       3.61241 /  2.55 ( 2045)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1732.56 seconds
wall clock time: 30 minutes 53.48 seconds (1853.48 seconds total)