Starting phenix.real_space_refine
on Wed Mar  4 15:12:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pf4_13367/03_2026/7pf4_13367.map"
  }
  resolution = 4.0
  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=  -0.000 sd=   0.003
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    7084      2.51       5
     N    2431      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 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: "J"
      Number of atoms: 3442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3442
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "I"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3405
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 2.64, per 1000 atoms: 0.20
  Number of scatterers: 12935
  At special positions: 0
  Unit cell: (116.55, 152.25, 117.6, 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    2431      7.00
     C    7084      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: 1.02
  Conformation dependent library (CDL) restraints added in 363.3 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 8 sheets defined
      71.1% alpha, 2.1% beta
      165 base pairs and 285 stacking pairs defined.
    Time for finding SS restraints: 2.14
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.711A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 3.614A  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: 3.781A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 3.992A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 4.207A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 94
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 36
      removed outlier: 3.668A  pdb=" N   VAL M  30 " --> pdb=" O   PRO M  26 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.053A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 37 through 49
      removed outlier: 3.550A  pdb=" N   VAL N  41 " --> pdb=" O   TYR N  37 " (cutoff:3.500A)
    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 79
      removed outlier: 3.764A  pdb=" N   PHE O  78 " --> pdb=" O   ILE O  74 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
    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: 3.759A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
    Processing helix  chain 'Q' and resid 16 through 21
    Processing helix  chain 'Q' and resid 26 through 36
      removed outlier: 3.669A  pdb=" N   VAL Q  30 " --> pdb=" O   PRO Q  26 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.285A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
    Processing helix  chain 'Q' and resid 90 through 97
    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 103 through 123
      removed outlier: 3.695A  pdb=" N   ALA R 107 " --> pdb=" O   PRO R 103 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS R 108 " --> pdb=" O   GLY R 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.735A  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 'M' and resid 42 through 43
      removed outlier: 7.229A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.675A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.181A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 77 through 78

    399 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      423 hydrogen bonds
      846 hydrogen bond angles
      0 basepair planarities
      165 basepair parallelities
      285 stacking parallelities
  Total time for adding SS restraints: 3.14

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2644
        1.34 -     1.46: 4652
        1.46 -     1.58: 5866
        1.58 -     1.70: 666
        1.70 -     1.82: 20
  Bond restraints: 13848
  Sorted by residual:
  bond pdb=" C3'  DG I 522 "
       pdb=" O3'  DG I 522 "
    ideal  model  delta    sigma   weight residual
    1.422  1.485 -0.063 3.00e-02 1.11e+03 4.35e+00
  bond pdb=" C3'  DG I 410 "
       pdb=" O3'  DG I 410 "
    ideal  model  delta    sigma   weight residual
    1.422  1.481 -0.059 3.00e-02 1.11e+03 3.85e+00
  bond pdb=" C3'  DG I 488 "
       pdb=" O3'  DG I 488 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 3.00e-02 1.11e+03 3.57e+00
  bond pdb=" C3'  DT I 502 "
       pdb=" O3'  DT I 502 "
    ideal  model  delta    sigma   weight residual
    1.422  1.471 -0.049 3.00e-02 1.11e+03 2.62e+00
  bond pdb=" CG  GLU K 105 "
       pdb=" CD  GLU K 105 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.23e+00
  ... (remaining 13843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 19742
        2.52 -     5.03: 338
        5.03 -     7.55: 43
        7.55 -    10.06: 10
       10.06 -    12.58: 2
  Bond angle restraints: 20135
  Sorted by residual:
  angle pdb=" CA  GLU K  97 "
        pdb=" CB  GLU K  97 "
        pdb=" CG  GLU K  97 "
      ideal   model   delta    sigma   weight residual
     114.10  126.68  -12.58 2.00e+00 2.50e-01 3.95e+01
  angle pdb=" C   ILE M  87 "
        pdb=" N   ARG M  88 "
        pdb=" CA  ARG M  88 "
      ideal   model   delta    sigma   weight residual
     122.73  112.87    9.86 1.61e+00 3.86e-01 3.75e+01
  angle pdb=" N   GLU K  97 "
        pdb=" CA  GLU K  97 "
        pdb=" CB  GLU K  97 "
      ideal   model   delta    sigma   weight residual
     110.28  118.73   -8.45 1.55e+00 4.16e-01 2.97e+01
  angle pdb=" N   GLU K 105 "
        pdb=" CA  GLU K 105 "
        pdb=" CB  GLU K 105 "
      ideal   model   delta    sigma   weight residual
     110.16  117.55   -7.39 1.48e+00 4.57e-01 2.49e+01
  angle pdb=" CA  LYS M 118 "
        pdb=" CB  LYS M 118 "
        pdb=" CG  LYS M 118 "
      ideal   model   delta    sigma   weight residual
     114.10  122.32   -8.22 2.00e+00 2.50e-01 1.69e+01
  ... (remaining 20130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.22: 5688
       35.22 -    70.44: 1736
       70.44 -   105.66: 33
      105.66 -   140.88: 2
      140.88 -   176.09: 1
  Dihedral angle restraints: 7460
    sinusoidal: 5238
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  ARG L  23 "
           pdb=" C   ARG L  23 "
           pdb=" N   ASP L  24 "
           pdb=" CA  ASP L  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.36  -30.64     0      5.00e+00 4.00e-02 3.76e+01
  dihedral pdb=" CA  ARG M  88 "
           pdb=" C   ARG M  88 "
           pdb=" N   ASN M  89 "
           pdb=" CA  ASN M  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  PRO M  26 "
           pdb=" C   PRO M  26 "
           pdb=" N   VAL M  27 "
           pdb=" CA  VAL M  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 7457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1793
       0.051 -    0.102: 403
       0.102 -    0.153: 71
       0.153 -    0.205: 14
       0.205 -    0.256: 7
  Chirality restraints: 2288
  Sorted by residual:
  chirality pdb=" CA  GLU K  97 "
            pdb=" N   GLU K  97 "
            pdb=" C   GLU K  97 "
            pdb=" CB  GLU K  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  PHE K 104 "
            pdb=" N   PHE K 104 "
            pdb=" C   PHE K 104 "
            pdb=" CB  PHE K 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CG  LEU N  45 "
            pdb=" CB  LEU N  45 "
            pdb=" CD1 LEU N  45 "
            pdb=" CD2 LEU N  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 2285 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE M  25 "    0.065 5.00e-02 4.00e+02   9.96e-02 1.59e+01
        pdb=" N   PRO M  26 "   -0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO M  26 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO M  26 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M  79 "   -0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO M  80 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO M  80 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO M  80 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS N  85 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   LYS N  85 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LYS N  85 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG N  86 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2610
        2.79 -     3.31: 11699
        3.31 -     3.84: 27751
        3.84 -     4.37: 30869
        4.37 -     4.90: 42548
  Nonbonded interactions: 115477
  Sorted by model distance:
  nonbonded pdb=" O   THR M  76 "
            pdb=" OG1 THR N  52 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG L  78 "
            pdb=" O   THR L  80 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" N   GLY Q  44 "
            pdb=" O   ILE R  89 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OH  TYR Q  39 "
            pdb=" OE1 GLU R  71 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" N   GLY M  44 "
            pdb=" O   ILE N  89 "
     model   vdw
     2.336 3.120
  ... (remaining 115472 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:             1.760
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.460
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
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      :  0.005   0.063  13848  Z= 0.225
  Angle     :  0.887  12.577  20135  Z= 0.509
  Chirality :  0.047   0.256   2288
  Planarity :  0.007   0.100   1390
  Dihedral  : 29.722 176.094   6028
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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 : 0.14 %

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: -0.80 (0.27), residues: 752
  helix: -0.21 (0.20), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.02 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG P  45 
 TYR   0.038   0.003   TYR O  99 
 PHE   0.021   0.003   PHE N  65 
 HIS   0.008   0.002   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (13848)
  covalent geometry    : angle       0.88700 (20135)
  hydrogen bonds       : bond        0.09572 (  822)
  hydrogen bonds       : angle       4.76338 ( 2034)

*********************** 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
  168 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: K   96 SER cc_start: 0.9070 (m) cc_final: 0.8859 (p)
REVERT: K   99 TYR cc_start: 0.8859 (t80) cc_final: 0.8502 (t80)
REVERT: K  106 ASP cc_start: 0.8751 (m-30) cc_final: 0.8529 (m-30)
REVERT: L   49 LEU cc_start: 0.8979 (mp) cc_final: 0.8723 (mp)
REVERT: M   25 PHE cc_start: 0.7803 (m-80) cc_final: 0.7570 (m-10)
REVERT: N   52 THR cc_start: 0.8016 (t) cc_final: 0.7471 (t)
REVERT: N   71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8272 (tt0)
REVERT: N   95 GLN cc_start: 0.8630 (pp30) cc_final: 0.8074 (tm-30)
REVERT: N  105 GLU cc_start: 0.7939 (tp30) cc_final: 0.7627 (tp30)
REVERT: N  108 LYS cc_start: 0.9269 (ptmm) cc_final: 0.8529 (ptmm)
REVERT: N  116 LYS cc_start: 0.9457 (tmmt) cc_final: 0.8431 (tmtt)
REVERT: O   97 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: Q   79 ILE cc_start: 0.8482 (mm) cc_final: 0.7912 (pt)
REVERT: R   51 ASP cc_start: 0.8340 (p0) cc_final: 0.8092 (p0)
REVERT: R   95 GLN cc_start: 0.8624 (tm130) cc_final: 0.8363 (tm-30)
REVERT: R  102 LEU cc_start: 0.9333 (mt) cc_final: 0.9091 (mp)
REVERT: R  105 GLU cc_start: 0.8324 (mp0) cc_final: 0.7884 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1168
  time to fit residues: 27.9660
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0020
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** K  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  84 GLN
N  82 HIS
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
O  93 GLN
R  47 GLN
** R  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.064153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.052297 restraints weight = 118378.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.053489 restraints weight = 68657.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.054233 restraints weight = 47432.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.054755 restraints weight = 36967.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.055103 restraints weight = 31219.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13848  Z= 0.169
  Angle     :  0.656  10.168  20135  Z= 0.387
  Chirality :  0.037   0.188   2288
  Planarity :  0.005   0.068   1390
  Dihedral  : 32.363 172.566   4504
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.59 %
    Favored  : 89.31 %
  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:  0.56 (0.29), residues: 752
  helix:  0.85 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.66 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R  86 
 TYR   0.017   0.002   TYR R  40 
 PHE   0.017   0.002   PHE P  61 
 HIS   0.011   0.002   HIS N  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (13848)
  covalent geometry    : angle       0.65616 (20135)
  hydrogen bonds       : bond        0.04147 (  822)
  hydrogen bonds       : angle       3.38042 ( 2034)

*********************** 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
  152 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  100 LEU cc_start: 0.9241 (mt) cc_final: 0.8607 (mm)
REVERT: K  104 PHE cc_start: 0.9246 (m-10) cc_final: 0.8712 (m-80)
REVERT: K  105 GLU cc_start: 0.8812 (mp0) cc_final: 0.8559 (mp0)
REVERT: L   59 LYS cc_start: 0.9031 (tppt) cc_final: 0.8774 (tppp)
REVERT: M   91 GLU cc_start: 0.7828 (tp30) cc_final: 0.7620 (tp30)
REVERT: N   85 LYS cc_start: 0.9271 (ttpt) cc_final: 0.8968 (ttpp)
REVERT: N  108 LYS cc_start: 0.9365 (ptmm) cc_final: 0.8936 (ptmm)
REVERT: O   54 TYR cc_start: 0.8479 (m-80) cc_final: 0.8132 (m-80)
REVERT: O  100 LEU cc_start: 0.9233 (mt) cc_final: 0.8997 (mt)
REVERT: O  104 PHE cc_start: 0.9053 (m-10) cc_final: 0.8792 (m-10)
REVERT: R  108 LYS cc_start: 0.9378 (mtmt) cc_final: 0.9138 (mtmm)
  outliers start: 7
  outliers final: 4
  residues processed: 149
  average time/residue: 0.1223
  time to fit residues: 25.8201
Evaluate side-chains
  113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 9 optimal weight:    0.1980
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** K  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 HIS
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 108 ASN
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.064313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.052480 restraints weight = 118490.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.053674 restraints weight = 68344.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.054395 restraints weight = 46996.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.054904 restraints weight = 36750.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.055194 restraints weight = 31055.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13848  Z= 0.158
  Angle     :  0.621   7.811  20135  Z= 0.367
  Chirality :  0.035   0.162   2288
  Planarity :  0.005   0.060   1390
  Dihedral  : 32.172 171.533   4504
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.79 %
    Favored  : 86.48 %
  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:  1.08 (0.29), residues: 752
  helix:  1.28 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.62 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  92 
 TYR   0.024   0.002   TYR P  88 
 PHE   0.021   0.002   PHE P  61 
 HIS   0.007   0.001   HIS N  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13848)
  covalent geometry    : angle       0.62064 (20135)
  hydrogen bonds       : bond        0.03884 (  822)
  hydrogen bonds       : angle       3.15525 ( 2034)

*********************** 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
  141 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   99 TYR cc_start: 0.8270 (t80) cc_final: 0.8056 (t80)
REVERT: K  104 PHE cc_start: 0.9047 (m-10) cc_final: 0.8593 (m-10)
REVERT: K  105 GLU cc_start: 0.8705 (mp0) cc_final: 0.8443 (mp0)
REVERT: L   59 LYS cc_start: 0.9023 (tppt) cc_final: 0.8715 (tppp)
REVERT: M   91 GLU cc_start: 0.7876 (tp30) cc_final: 0.7635 (tp30)
REVERT: N   85 LYS cc_start: 0.9322 (ttpt) cc_final: 0.8974 (ttpp)
REVERT: N   95 GLN cc_start: 0.8569 (pp30) cc_final: 0.8077 (tm-30)
REVERT: N  105 GLU cc_start: 0.7966 (tp30) cc_final: 0.7526 (tp30)
REVERT: N  111 VAL cc_start: 0.8948 (t) cc_final: 0.8627 (p)
REVERT: N  120 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8387 (mmtt)
REVERT: O   54 TYR cc_start: 0.8478 (m-80) cc_final: 0.8226 (m-80)
REVERT: O   55 GLN cc_start: 0.8808 (tp40) cc_final: 0.8537 (tp40)
REVERT: O  100 LEU cc_start: 0.9232 (mt) cc_final: 0.8926 (mt)
REVERT: O  104 PHE cc_start: 0.9118 (m-10) cc_final: 0.8755 (m-10)
REVERT: R  108 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9099 (mtmm)
  outliers start: 11
  outliers final: 6
  residues processed: 137
  average time/residue: 0.1104
  time to fit residues: 21.8667
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue   79 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue  108 ASN
Chi-restraints excluded: chain P residue   21 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 110 ASN
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.055236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.043305 restraints weight = 107786.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.044331 restraints weight = 62823.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.045000 restraints weight = 43711.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.045443 restraints weight = 34561.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.045748 restraints weight = 29447.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  13848  Z= 0.294
  Angle     :  0.723  11.983  20135  Z= 0.422
  Chirality :  0.039   0.162   2288
  Planarity :  0.006   0.066   1390
  Dihedral  : 32.739 171.888   4504
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 22.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.84 %
    Favored  : 83.65 %
  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:  0.90 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.79 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  42 
 TYR   0.040   0.004   TYR P  88 
 PHE   0.029   0.003   PHE P  61 
 HIS   0.009   0.002   HIS R  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 (13848)
  covalent geometry    : angle       0.72270 (20135)
  hydrogen bonds       : bond        0.08020 (  822)
  hydrogen bonds       : angle       3.83979 ( 2034)

*********************** 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
  125 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: K   99 TYR cc_start: 0.8734 (t80) cc_final: 0.8529 (t80)
REVERT: K  105 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8695 (mp0)
REVERT: L   59 LYS cc_start: 0.9223 (tppt) cc_final: 0.8973 (tppp)
REVERT: M   92 GLU cc_start: 0.8751 (pm20) cc_final: 0.8439 (pm20)
REVERT: N   85 LYS cc_start: 0.9434 (ttpt) cc_final: 0.9093 (ttpp)
REVERT: N  120 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8824 (mmtp)
REVERT: O   54 TYR cc_start: 0.8820 (m-80) cc_final: 0.8567 (m-80)
REVERT: O   97 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: O  104 PHE cc_start: 0.9238 (m-10) cc_final: 0.8811 (m-10)
REVERT: R  108 LYS cc_start: 0.9507 (mtmt) cc_final: 0.9233 (mtmm)
  outliers start: 16
  outliers final: 7
  residues processed: 120
  average time/residue: 0.1148
  time to fit residues: 19.9704
Evaluate side-chains
  103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain M residue   87 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   44 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  39 HIS
** Q  84 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.060843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.049038 restraints weight = 120189.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.050190 restraints weight = 68759.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.050969 restraints weight = 46807.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.051454 restraints weight = 35989.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.051819 restraints weight = 30528.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13848  Z= 0.170
  Angle     :  0.641  11.316  20135  Z= 0.376
  Chirality :  0.035   0.151   2288
  Planarity :  0.005   0.060   1390
  Dihedral  : 32.437 173.036   4504
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 17.14 %
    Favored  : 81.92 %
  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:  1.04 (0.30), residues: 752
  helix:  1.26 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  42 
 TYR   0.026   0.002   TYR M  57 
 PHE   0.020   0.002   PHE O  67 
 HIS   0.006   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13848)
  covalent geometry    : angle       0.64084 (20135)
  hydrogen bonds       : bond        0.04196 (  822)
  hydrogen bonds       : angle       3.34557 ( 2034)

*********************** 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
  122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   61 GLU cc_start: 0.9041 (tp30) cc_final: 0.8829 (tp30)
REVERT: N   85 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9022 (ttpp)
REVERT: O   55 GLN cc_start: 0.8984 (tp40) cc_final: 0.8521 (mm-40)
REVERT: O  104 PHE cc_start: 0.9080 (m-10) cc_final: 0.8558 (m-10)
REVERT: R  108 LYS cc_start: 0.9361 (mtmt) cc_final: 0.9100 (mtmm)
  outliers start: 6
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1139
  time to fit residues: 20.1085
Evaluate side-chains
  110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain R residue   48 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 46 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  93 GLN
** Q  84 GLN ** 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 = 0.3830 r_free = 0.3830 target = 0.061388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.049700 restraints weight = 119291.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.050850 restraints weight = 68311.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.051602 restraints weight = 46851.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.052002 restraints weight = 36298.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.052320 restraints weight = 31287.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13848  Z= 0.165
  Angle     :  0.621   8.296  20135  Z= 0.365
  Chirality :  0.034   0.156   2288
  Planarity :  0.005   0.060   1390
  Dihedral  : 32.150 171.214   4504
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.45 %
    Favored  : 80.66 %
  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:  1.13 (0.30), residues: 752
  helix:  1.23 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.46 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  42 
 TYR   0.023   0.002   TYR M  57 
 PHE   0.020   0.002   PHE P  61 
 HIS   0.005   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (13848)
  covalent geometry    : angle       0.62114 (20135)
  hydrogen bonds       : bond        0.04100 (  822)
  hydrogen bonds       : angle       3.27086 ( 2034)

*********************** 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
  121 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8807 (mm-30)
REVERT: N   85 LYS cc_start: 0.9281 (ttpt) cc_final: 0.8933 (ttpp)
REVERT: N  111 VAL cc_start: 0.9100 (t) cc_final: 0.8721 (p)
REVERT: N  120 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8655 (mmtt)
REVERT: O   55 GLN cc_start: 0.8999 (tp40) cc_final: 0.8462 (mm-40)
REVERT: R   85 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9117 (mmtp)
REVERT: R  108 LYS cc_start: 0.9339 (mtmt) cc_final: 0.9062 (mtmm)
  outliers start: 12
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1113
  time to fit residues: 19.3618
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   80 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 83 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
O  93 GLN
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.056456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.044523 restraints weight = 106634.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.045610 restraints weight = 61424.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.046292 restraints weight = 42252.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.046761 restraints weight = 33160.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.047000 restraints weight = 28168.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13848  Z= 0.216
  Angle     :  0.669  11.994  20135  Z= 0.387
  Chirality :  0.036   0.252   2288
  Planarity :  0.005   0.061   1390
  Dihedral  : 32.318 170.901   4504
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.97 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.01 (0.30), residues: 752
  helix:  1.13 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.45 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  42 
 TYR   0.020   0.002   TYR O  99 
 PHE   0.045   0.004   PHE P  61 
 HIS   0.008   0.001   HIS R  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (13848)
  covalent geometry    : angle       0.66917 (20135)
  hydrogen bonds       : bond        0.05570 (  822)
  hydrogen bonds       : angle       3.52539 ( 2034)

*********************** 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
  121 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.8546 (m-80) cc_final: 0.8307 (m-80)
REVERT: M   92 GLU cc_start: 0.8514 (pm20) cc_final: 0.8276 (pm20)
REVERT: N   85 LYS cc_start: 0.9355 (ttpt) cc_final: 0.9002 (ttpp)
REVERT: N  111 VAL cc_start: 0.9297 (t) cc_final: 0.8992 (p)
REVERT: N  120 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8643 (mmtp)
REVERT: O   55 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8967 (tp40)
REVERT: O  104 PHE cc_start: 0.9224 (m-10) cc_final: 0.8898 (m-10)
REVERT: R   85 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9263 (mmtp)
REVERT: R  108 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9222 (mtmt)
  outliers start: 13
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1105
  time to fit residues: 18.9662
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   26 ILE
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue   87 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   55 GLN
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   80 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
O  93 GLN
P  93 GLN
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.055051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.043373 restraints weight = 106301.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.044435 restraints weight = 61110.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.045131 restraints weight = 42119.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.045593 restraints weight = 32901.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.045893 restraints weight = 27823.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13848  Z= 0.231
  Angle     :  0.696  12.979  20135  Z= 0.401
  Chirality :  0.036   0.207   2288
  Planarity :  0.005   0.061   1390
  Dihedral  : 32.431 171.861   4504
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.60 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.80 (0.30), residues: 752
  helix:  0.98 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.55 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O  52 
 TYR   0.032   0.002   TYR M  57 
 PHE   0.035   0.003   PHE P  61 
 HIS   0.007   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (13848)
  covalent geometry    : angle       0.69642 (20135)
  hydrogen bonds       : bond        0.05773 (  822)
  hydrogen bonds       : angle       3.68359 ( 2034)

*********************** 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
  126 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.8500 (m-80) cc_final: 0.8225 (m-80)
REVERT: M   15 LYS cc_start: 0.8501 (tptp) cc_final: 0.8288 (tptt)
REVERT: M   92 GLU cc_start: 0.8528 (pm20) cc_final: 0.8256 (pm20)
REVERT: N   85 LYS cc_start: 0.9373 (ttpt) cc_final: 0.9033 (ttpp)
REVERT: N   89 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: N  120 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8671 (mmtp)
REVERT: O  104 PHE cc_start: 0.9293 (m-10) cc_final: 0.8934 (m-10)
REVERT: Q   84 GLN cc_start: 0.5548 (tm-30) cc_final: 0.5338 (tm-30)
REVERT: R  108 LYS cc_start: 0.9467 (mtmt) cc_final: 0.9222 (mtmt)
  outliers start: 12
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1041
  time to fit residues: 18.6772
Evaluate side-chains
  119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   26 ILE
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   89 ILE
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   80 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  38 ASN
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** 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 = 0.3790 r_free = 0.3790 target = 0.059393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.047960 restraints weight = 122139.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.049107 restraints weight = 69068.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.049811 restraints weight = 46890.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.050318 restraints weight = 36373.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.050713 restraints weight = 30542.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  13848  Z= 0.174
  Angle     :  0.665  12.341  20135  Z= 0.383
  Chirality :  0.035   0.262   2288
  Planarity :  0.005   0.060   1390
  Dihedral  : 32.260 169.563   4504
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 21.23 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.30), residues: 752
  helix:  1.17 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.47 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N  99 
 TYR   0.026   0.002   TYR M  57 
 PHE   0.033   0.003   PHE P  61 
 HIS   0.005   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (13848)
  covalent geometry    : angle       0.66464 (20135)
  hydrogen bonds       : bond        0.04157 (  822)
  hydrogen bonds       : angle       3.46412 ( 2034)

*********************** 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
  128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   92 GLU cc_start: 0.8518 (pm20) cc_final: 0.8246 (pm20)
REVERT: N   85 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8961 (ttpp)
REVERT: N  111 VAL cc_start: 0.9229 (t) cc_final: 0.9014 (p)
REVERT: O   54 TYR cc_start: 0.8541 (m-80) cc_final: 0.8107 (m-80)
REVERT: O  104 PHE cc_start: 0.9194 (m-10) cc_final: 0.8896 (m-10)
  outliers start: 9
  outliers final: 9
  residues processed: 126
  average time/residue: 0.0928
  time to fit residues: 17.4438
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   26 ILE
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   48 VAL
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:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 96 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.055638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.043931 restraints weight = 107828.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.045008 restraints weight = 61011.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.045706 restraints weight = 42014.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.046206 restraints weight = 32621.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.046536 restraints weight = 27406.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.5608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13848  Z= 0.203
  Angle     :  0.689  12.401  20135  Z= 0.396
  Chirality :  0.036   0.237   2288
  Planarity :  0.005   0.061   1390
  Dihedral  : 32.311 169.842   4504
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.17 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.30), residues: 752
  helix:  0.97 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.54 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N  99 
 TYR   0.014   0.002   TYR O  99 
 PHE   0.039   0.003   PHE P  61 
 HIS   0.006   0.001   HIS N 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (13848)
  covalent geometry    : angle       0.68927 (20135)
  hydrogen bonds       : bond        0.05251 (  822)
  hydrogen bonds       : angle       3.61295 ( 2034)

********************** 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
  122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   92 GLU cc_start: 0.8535 (pm20) cc_final: 0.8279 (pm20)
REVERT: N   85 LYS cc_start: 0.9327 (ttpt) cc_final: 0.9012 (ttpp)
REVERT: N   89 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7709 (tp)
REVERT: N   95 GLN cc_start: 0.8854 (pp30) cc_final: 0.8123 (pp30)
REVERT: N  111 VAL cc_start: 0.9341 (t) cc_final: 0.8994 (p)
REVERT: N  120 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8922 (mmtt)
REVERT: O   54 TYR cc_start: 0.8759 (m-80) cc_final: 0.8307 (m-80)
REVERT: O  104 PHE cc_start: 0.9283 (m-10) cc_final: 0.8925 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 119
  average time/residue: 0.1093
  time to fit residues: 19.1484
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain L residue   26 ILE
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue   89 ILE
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   34 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   80 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 GLN
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.056934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.045246 restraints weight = 105319.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.046354 restraints weight = 60065.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.047069 restraints weight = 41092.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.047522 restraints weight = 31989.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.047861 restraints weight = 27206.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13848  Z= 0.174
  Angle     :  0.682  12.504  20135  Z= 0.389
  Chirality :  0.036   0.272   2288
  Planarity :  0.005   0.059   1390
  Dihedral  : 32.198 168.573   4504
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.64 %
    Favored  : 75.47 %
  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:  0.96 (0.30), residues: 752
  helix:  1.10 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.45 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N  99 
 TYR   0.017   0.002   TYR L  72 
 PHE   0.049   0.003   PHE P  61 
 HIS   0.004   0.001   HIS N 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (13848)
  covalent geometry    : angle       0.68205 (20135)
  hydrogen bonds       : bond        0.04209 (  822)
  hydrogen bonds       : angle       3.49474 ( 2034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2055.06 seconds
wall clock time: 36 minutes 16.48 seconds (2176.48 seconds total)