Starting phenix.real_space_refine
on Sat Sep 12 07:25:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pff_13374/09_2026/7pff_13374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pff_13374/09_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_13374/09_2026/7pff_13374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pff_13374/09_2026/7pff_13374.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pff_13374/09_2026/7pff_13374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pff_13374/09_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.76, per 1000 atoms: 0.21
  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: 1.03
  Conformation dependent library (CDL) restraints added in 339.4 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: 2.00
  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: 3.13

  Time building geometry restraints manager: 1.43 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=" O3'  DC I 563 "
       pdb=" P    DT I 564 "
    ideal  model  delta    sigma   weight residual
    1.607  1.665 -0.058 1.20e-02 6.94e+03 2.30e+01
  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=" 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: 19078
        2.23 -     4.47: 966
        4.47 -     6.70: 72
        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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.670
  Find NCS groups from input model:        0.130
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.250
-------------------------------------------------------------------------------
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= 0.645
  Angle     :  1.058  11.167  20135  Z= 0.866
  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 /  0.65 (13848)
  covalent geometry    : angle       1.05758 /  0.87 (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  : 0.332 
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: 0.1052
  time to fit residues: 14.4697
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  : 0.326 
-------------------------------------------------------------------------------
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...
M  84 GLN
N 109 HIS
O  76 GLN
P  25 ASN
R 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.037595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.031365 restraints weight = 193472.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.032315 restraints weight = 111925.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.032972 restraints weight = 74907.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.033440 restraints weight = 54683.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.033752 restraints weight = 42704.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1013

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     :  0.787   9.888  20135  Z= 0.456
  Chirality :  0.054   0.364   2288
  Planarity :  0.006   0.065   1390
  Dihedral  : 33.873 178.893   4508
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.26 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.58 (0.29), residues: 752
  helix:  0.72 (0.21), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  95 
 TYR   0.015   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        0.00279 /  0.18 (13848)
  covalent geometry    : angle       0.78699 /  0.46 (20135)
  hydrogen bonds       : bond        0.06915 /  4.82 (  828)
  hydrogen bonds       : angle       3.89263 /  2.77 ( 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
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9481 (m-80) cc_final: 0.9047 (m-80)
REVERT: K  100 LEU cc_start: 0.9902 (mt) cc_final: 0.9650 (mt)
REVERT: K  104 PHE cc_start: 0.9717 (m-10) cc_final: 0.9457 (m-80)
REVERT: K  105 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9459 (mt-10)
REVERT: N  109 HIS cc_start: 0.9453 (m90) cc_final: 0.9117 (m90)
REVERT: O   54 TYR cc_start: 0.9048 (m-80) cc_final: 0.8749 (m-80)
REVERT: O  104 PHE cc_start: 0.9461 (m-80) cc_final: 0.9235 (m-80)
REVERT: Q   26 PRO cc_start: 0.7317 (Cg_endo) cc_final: 0.7038 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9048 (tp) cc_final: 0.8717 (tp)
REVERT: R  109 HIS cc_start: 0.9528 (m90) cc_final: 0.9021 (m-70)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1042
  time to fit residues: 12.9777
Evaluate side-chains
  57 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 93 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 97 optimal weight:   30.0000
   chunk 9 optimal weight:    0.0870
   chunk 81 optimal weight:   30.0000
   overall best weight:    2.3764

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.044263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.031931 restraints weight = 138955.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.033269 restraints weight = 91082.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.034274 restraints weight = 67504.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.035039 restraints weight = 53711.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.035644 restraints weight = 44882.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13848  Z= 0.169
  Angle     :  0.735   8.760  20135  Z= 0.430
  Chirality :  0.051   0.332   2288
  Planarity :  0.005   0.062   1390
  Dihedral  : 33.771 172.087   4508
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.73 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.29), residues: 752
  helix:  0.95 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.08 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.022   0.002   TYR Q  57 
 PHE   0.010   0.002   PHE N  65 
 HIS   0.003   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.17 (13848)
  covalent geometry    : angle       0.73474 /  0.43 (20135)
  hydrogen bonds       : bond        0.06892 /  4.75 (  828)
  hydrogen bonds       : angle       3.72673 /  2.64 ( 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
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9454 (m-80) cc_final: 0.9076 (m-80)
REVERT: K  100 LEU cc_start: 0.9912 (mt) cc_final: 0.9637 (mp)
REVERT: K  104 PHE cc_start: 0.9727 (m-10) cc_final: 0.9500 (m-80)
REVERT: K  105 GLU cc_start: 0.9638 (mt-10) cc_final: 0.9413 (mt-10)
REVERT: N  108 LYS cc_start: 0.9602 (ptpp) cc_final: 0.9362 (ptpt)
REVERT: N  109 HIS cc_start: 0.9216 (m90) cc_final: 0.8866 (m90)
REVERT: O   54 TYR cc_start: 0.8936 (m-80) cc_final: 0.8701 (m-80)
REVERT: O  104 PHE cc_start: 0.9436 (m-80) cc_final: 0.9212 (m-80)
REVERT: Q   26 PRO cc_start: 0.7092 (Cg_endo) cc_final: 0.6797 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9214 (tp) cc_final: 0.8866 (tp)
REVERT: R  105 GLU cc_start: 0.9576 (tp30) cc_final: 0.9364 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1026
  time to fit residues: 12.8563
Evaluate side-chains
  63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 99 optimal weight:   30.0000
   chunk 73 optimal weight:   30.0000
   chunk 4 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 87 optimal weight:   40.0000
   chunk 45 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3475 r_free = 0.3475 target = 0.036668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.029469 restraints weight = 172772.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.030398 restraints weight = 105409.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.031021 restraints weight = 73688.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.031496 restraints weight = 56660.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.031849 restraints weight = 45715.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13848  Z= 0.157
  Angle     :  0.708   9.577  20135  Z= 0.413
  Chirality :  0.049   0.324   2288
  Planarity :  0.005   0.061   1390
  Dihedral  : 33.753 172.356   4508
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.99 %
    Favored  : 96.86 %
  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:  1.23 (0.29), residues: 752
  helix:  1.19 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.00 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  35 
 TYR   0.015   0.001   TYR L  51 
 PHE   0.009   0.001   PHE R  70 
 HIS   0.005   0.001   HIS O 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.16 (13848)
  covalent geometry    : angle       0.70810 /  0.41 (20135)
  hydrogen bonds       : bond        0.05910 /  4.09 (  828)
  hydrogen bonds       : angle       3.58503 /  2.54 ( 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
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9439 (m-80) cc_final: 0.9063 (m-80)
REVERT: K  100 LEU cc_start: 0.9910 (mt) cc_final: 0.9642 (mp)
REVERT: K  104 PHE cc_start: 0.9716 (m-10) cc_final: 0.9474 (m-80)
REVERT: N  108 LYS cc_start: 0.9651 (ptpp) cc_final: 0.9370 (pttm)
REVERT: N  109 HIS cc_start: 0.9410 (m90) cc_final: 0.9027 (m90)
REVERT: O   54 TYR cc_start: 0.8938 (m-80) cc_final: 0.8670 (m-80)
REVERT: P   74 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9373 (tm-30)
REVERT: Q   26 PRO cc_start: 0.7098 (Cg_endo) cc_final: 0.6800 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9124 (tp) cc_final: 0.8838 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 82
  average time/residue: 0.1020
  time to fit residues: 12.9113
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.043486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.031588 restraints weight = 139155.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.032898 restraints weight = 90257.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.033859 restraints weight = 66812.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.034594 restraints weight = 53311.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.035156 restraints weight = 44655.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  13848  Z= 0.185
  Angle     :  0.728  10.095  20135  Z= 0.421
  Chirality :  0.049   0.308   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 33.763 171.186   4508
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.24 (0.30), residues: 752
  helix:  1.23 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.08 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.015   0.002   TYR L  51 
 PHE   0.017   0.002   PHE K 104 
 HIS   0.003   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.18 (13848)
  covalent geometry    : angle       0.72810 /  0.42 (20135)
  hydrogen bonds       : bond        0.07804 /  5.35 (  828)
  hydrogen bonds       : angle       3.69673 /  2.63 ( 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
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  108 ASN cc_start: 0.8290 (t0) cc_final: 0.8005 (p0)
REVERT: Q   26 PRO cc_start: 0.7821 (Cg_endo) cc_final: 0.7606 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0968
  time to fit residues: 12.3280
Evaluate side-chains
  54 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 97 optimal weight:   40.0000
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:   30.0000
   chunk 46 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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
P  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.035784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.029758 restraints weight = 204514.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.030629 restraints weight = 118156.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.031211 restraints weight = 79786.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.031660 restraints weight = 59094.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.032013 restraints weight = 46274.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2280

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= 0.204
  Angle     :  0.746  11.039  20135  Z= 0.431
  Chirality :  0.050   0.301   2288
  Planarity :  0.005   0.064   1390
  Dihedral  : 33.898 170.836   4508
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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:  1.18 (0.30), residues: 752
  helix:  1.22 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.20 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  36 
 TYR   0.024   0.002   TYR O  54 
 PHE   0.017   0.003   PHE O 104 
 HIS   0.012   0.002   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.20 (13848)
  covalent geometry    : angle       0.74614 /  0.43 (20135)
  hydrogen bonds       : bond        0.08716 /  5.97 (  828)
  hydrogen bonds       : angle       3.84033 /  2.71 ( 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
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9468 (m-80) cc_final: 0.9019 (m-80)
REVERT: K  104 PHE cc_start: 0.9673 (m-80) cc_final: 0.9340 (m-80)
REVERT: K  108 ASN cc_start: 0.9127 (t0) cc_final: 0.8330 (p0)
REVERT: N  109 HIS cc_start: 0.9481 (m90) cc_final: 0.9094 (m90)
REVERT: O  104 PHE cc_start: 0.9482 (m-80) cc_final: 0.9263 (m-80)
REVERT: P   74 GLU cc_start: 0.9489 (tm-30) cc_final: 0.9288 (tm-30)
REVERT: Q   26 PRO cc_start: 0.7140 (Cg_endo) cc_final: 0.6853 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.9027 (tp) cc_final: 0.8660 (tp)
REVERT: R  105 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: R  106 LEU cc_start: 0.9146 (mt) cc_final: 0.8795 (mt)
REVERT: R  109 HIS cc_start: 0.9630 (m90) cc_final: 0.9247 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0959
  time to fit residues: 11.6866
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  : 0.327 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 83 optimal weight:   30.0000
   chunk 21 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:   30.0000
   chunk 52 optimal weight:    0.6980
   chunk 76 optimal weight:   30.0000
   chunk 41 optimal weight:    3.9990
   overall best weight:    3.7386

-------------------------------------------------------------------------------
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 = 0.3474 r_free = 0.3474 target = 0.035633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.029649 restraints weight = 204610.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.030522 restraints weight = 117706.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.031117 restraints weight = 79154.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.031542 restraints weight = 58245.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.031878 restraints weight = 45797.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2484

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= 0.193
  Angle     :  0.738  11.165  20135  Z= 0.425
  Chirality :  0.050   0.299   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 33.943 170.671   4508
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  1.02 (0.29), residues: 752
  helix:  1.13 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.36 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  95 
 TYR   0.013   0.002   TYR O  54 
 PHE   0.010   0.002   PHE R  70 
 HIS   0.004   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.19 (13848)
  covalent geometry    : angle       0.73809 /  0.43 (20135)
  hydrogen bonds       : bond        0.08105 /  5.55 (  828)
  hydrogen bonds       : angle       3.89048 /  2.75 ( 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
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9443 (m-80) cc_final: 0.9034 (m-80)
REVERT: K  104 PHE cc_start: 0.9671 (m-80) cc_final: 0.9381 (m-80)
REVERT: K  108 ASN cc_start: 0.9126 (t0) cc_final: 0.8361 (p0)
REVERT: N  109 HIS cc_start: 0.9460 (m90) cc_final: 0.9095 (m90)
REVERT: O  104 PHE cc_start: 0.9505 (m-80) cc_final: 0.9276 (m-80)
REVERT: P   74 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9285 (tm-30)
REVERT: Q   26 PRO cc_start: 0.6747 (Cg_endo) cc_final: 0.6335 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8975 (tp) cc_final: 0.8721 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1023
  time to fit residues: 12.1996
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  : 0.319 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 88 optimal weight:   50.0000
   chunk 53 optimal weight:    0.0470
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 74 optimal weight:   40.0000
   chunk 56 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8682

-------------------------------------------------------------------------------
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 ** 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 = 0.3534 r_free = 0.3534 target = 0.037419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.031299 restraints weight = 193314.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.032172 restraints weight = 112048.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.032817 restraints weight = 76252.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.033301 restraints weight = 55843.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.033662 restraints weight = 43080.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13848  Z= 0.146
  Angle     :  0.697   9.727  20135  Z= 0.406
  Chirality :  0.049   0.305   2288
  Planarity :  0.004   0.059   1390
  Dihedral  : 33.774 169.730   4508
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  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:  1.24 (0.30), residues: 752
  helix:  1.28 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.25 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  86 
 TYR   0.022   0.001   TYR O  54 
 PHE   0.010   0.001   PHE R  70 
 HIS   0.003   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.15 (13848)
  covalent geometry    : angle       0.69708 /  0.41 (20135)
  hydrogen bonds       : bond        0.04911 /  3.37 (  828)
  hydrogen bonds       : angle       3.58095 /  2.54 ( 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
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9360 (m-80) cc_final: 0.8990 (m-80)
REVERT: K  104 PHE cc_start: 0.9637 (m-80) cc_final: 0.9390 (m-80)
REVERT: N   59 MET cc_start: 0.6651 (tpt) cc_final: 0.6354 (tpt)
REVERT: N  108 LYS cc_start: 0.9650 (ptpp) cc_final: 0.9402 (ptpt)
REVERT: N  109 HIS cc_start: 0.9450 (m90) cc_final: 0.9082 (m90)
REVERT: O  104 PHE cc_start: 0.9461 (m-80) cc_final: 0.9241 (m-80)
REVERT: P   74 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9291 (tm-30)
REVERT: Q   26 PRO cc_start: 0.6472 (Cg_endo) cc_final: 0.6043 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8923 (tp) cc_final: 0.8661 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0974
  time to fit residues: 12.7626
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  : 0.315 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:   30.0000
   chunk 30 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 103 optimal weight:   30.0000
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.036341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.030369 restraints weight = 200322.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.031261 restraints weight = 115884.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.031879 restraints weight = 77446.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.032321 restraints weight = 56711.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.032652 restraints weight = 44230.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13848  Z= 0.168
  Angle     :  0.716  10.448  20135  Z= 0.413
  Chirality :  0.048   0.285   2288
  Planarity :  0.004   0.060   1390
  Dihedral  : 33.719 168.876   4508
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  1.27 (0.30), residues: 752
  helix:  1.33 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.33 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.018   0.001   TYR O  54 
 PHE   0.009   0.001   PHE R  70 
 HIS   0.003   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.17 (13848)
  covalent geometry    : angle       0.71608 /  0.41 (20135)
  hydrogen bonds       : bond        0.06711 /  4.59 (  828)
  hydrogen bonds       : angle       3.67852 /  2.59 ( 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
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9388 (m-80) cc_final: 0.9018 (m-80)
REVERT: K  104 PHE cc_start: 0.9632 (m-10) cc_final: 0.9360 (m-80)
REVERT: N   71 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: N  108 LYS cc_start: 0.9652 (ptpp) cc_final: 0.9404 (pttm)
REVERT: N  109 HIS cc_start: 0.9469 (m90) cc_final: 0.9088 (m90)
REVERT: O  104 PHE cc_start: 0.9498 (m-80) cc_final: 0.9288 (m-80)
REVERT: P   74 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9318 (tm-30)
REVERT: Q   26 PRO cc_start: 0.6461 (Cg_endo) cc_final: 0.6045 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8918 (tp) cc_final: 0.8657 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1027
  time to fit residues: 12.6715
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  : 0.231 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 96 optimal weight:   30.0000
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.037442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.031357 restraints weight = 194634.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.032269 restraints weight = 112295.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.032918 restraints weight = 75080.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.033363 restraints weight = 54846.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.033716 restraints weight = 42874.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2914

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= 0.144
  Angle     :  0.691   9.992  20135  Z= 0.400
  Chirality :  0.048   0.298   2288
  Planarity :  0.004   0.058   1390
  Dihedral  : 33.634 166.515   4508
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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:  1.27 (0.30), residues: 752
  helix:  1.33 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.29 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG Q  88 
 TYR   0.021   0.001   TYR O  54 
 PHE   0.011   0.001   PHE R  70 
 HIS   0.003   0.001   HIS K 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.14 (13848)
  covalent geometry    : angle       0.69076 /  0.40 (20135)
  hydrogen bonds       : bond        0.04683 /  3.20 (  828)
  hydrogen bonds       : angle       3.53734 /  2.49 ( 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
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9436 (mt) cc_final: 0.9202 (mm)
REVERT: K   54 TYR cc_start: 0.9369 (m-80) cc_final: 0.9011 (m-80)
REVERT: K   94 GLU cc_start: 0.8912 (tp30) cc_final: 0.8625 (tp30)
REVERT: K  104 PHE cc_start: 0.9590 (m-10) cc_final: 0.9323 (m-80)
REVERT: N   71 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8565 (mm-30)
REVERT: N  108 LYS cc_start: 0.9646 (ptpp) cc_final: 0.9418 (ptpt)
REVERT: N  109 HIS cc_start: 0.9444 (m90) cc_final: 0.9063 (m-70)
REVERT: O   81 ASP cc_start: 0.9282 (m-30) cc_final: 0.9079 (m-30)
REVERT: P   74 GLU cc_start: 0.9496 (tm-30) cc_final: 0.9283 (tm-30)
REVERT: Q   26 PRO cc_start: 0.6311 (Cg_endo) cc_final: 0.5878 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8930 (tp) cc_final: 0.8668 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0941
  time to fit residues: 12.1314
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  : 0.336 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0970
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 74 optimal weight:   40.0000
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    4.0186

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.035705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.029826 restraints weight = 202325.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.030701 restraints weight = 116611.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.031318 restraints weight = 78129.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.031745 restraints weight = 57101.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.032085 restraints weight = 44684.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13848  Z= 0.199
  Angle     :  0.735  11.251  20135  Z= 0.421
  Chirality :  0.049   0.286   2288
  Planarity :  0.005   0.060   1390
  Dihedral  : 33.670 165.589   4508
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  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:  1.23 (0.30), residues: 752
  helix:  1.30 (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   0.006   0.001   ARG P  95 
 TYR   0.016   0.002   TYR O  54 
 PHE   0.008   0.001   PHE N  65 
 HIS   0.004   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.20 (13848)
  covalent geometry    : angle       0.73517 /  0.42 (20135)
  hydrogen bonds       : bond        0.08560 /  5.82 (  828)
  hydrogen bonds       : angle       3.75339 /  2.63 ( 2045)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.04 seconds
wall clock time: 32 minutes 54.58 seconds (1974.58 seconds total)