Starting phenix.real_space_refine
on Wed Feb  4 23:25:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uo5_26640/02_2026/7uo5_26640.cif"
  }
  resolution = 3.1
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      7      9.91       5
     P     372      5.49       5
     S       2      5.16       5
     C    4156      2.51       5
     N    1688      2.21       5
     O    2730      1.98       5
     H    5024      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13979
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 1898
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 12074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 12074
          Classifications: {'RNA': 373}
          Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 33, 'rna2p_pyr': 32, 'rna3p_pur': 185, 'rna3p_pyr': 123}
          Link IDs: {'rna2p': 64, 'rna3p': 308}
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' CA': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 47
    residue:
      pdb=" P     C B  20 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  20 " occ=0.00
    residue:
      pdb=" P     C B  21 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  21 " occ=0.00
    residue:
      pdb=" P     G B  22 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  22 " occ=0.00
    residue:
      pdb=" P     C B  23 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  23 " occ=0.00
    residue:
      pdb=" P     U B  24 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  24 " occ=0.00
    residue:
      pdb=" P     U B  25 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  25 " occ=0.00
    residue:
      pdb=" P     C B  26 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  26 " occ=0.00
    residue:
      pdb=" P     G B  27 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  27 " occ=0.00
    residue:
      pdb=" P     U B  28 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  28 " occ=0.00
    residue:
      pdb=" P     C B  29 " occ=0.00
      ... (29 atoms not shown)
      pdb=" H6    C B  29 " occ=0.00
    residue:
      pdb=" P     G B  30 " occ=0.00
      ... (32 atoms not shown)
      pdb=" H22   G B  30 " occ=0.00
    residue:
      pdb=" P     U B  31 " occ=0.00
      ... (28 atoms not shown)
      pdb=" H6    U B  31 " occ=0.00
    ... (remaining 35 not shown)
  Time building chain proxies: 2.79, per 1000 atoms: 0.20
  Number of scatterers: 13979
  At special positions: 0
  Unit cell: (89.7768, 120.107, 189.259, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      7     19.99
     S       2     16.00
     P     372     15.00
     O    2730      8.00
     N    1688      7.00
     C    4156      6.00
     H    5024      1.00
    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 164.0 milliseconds
  

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  214

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 1 sheets defined
      45.5% alpha, 17.9% beta
      96 base pairs and 146 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 13 through 23
      removed outlier: 3.602A  pdb=" N   PHE A  17 " --> pdb=" O   THR A  13 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A  20 " --> pdb=" O   GLN A  16 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 74
      removed outlier: 3.934A  pdb=" N   ASN A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 93
      removed outlier: 4.302A  pdb=" N   ALA A  93 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 93'
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 3.932A  pdb=" N   ALA A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LYS A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.511A  pdb=" N   ARG A  45 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   VAL A  86 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.698A  pdb=" N   ALA A  88 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 8.415A  pdb=" N   THR A  49 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)

    34 hydrogen bonds defined for protein.
    93 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      253 hydrogen bonds
      440 hydrogen bond angles
      0 basepair planarities
      96 basepair parallelities
      146 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 5023
        1.11 -     1.29: 488
        1.29 -     1.46: 5570
        1.46 -     1.64: 3868
        1.64 -     1.81: 3
  Bond restraints: 14952
  Sorted by residual:
  bond pdb=" C5    C B  10 "
       pdb=" H5    C B  10 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CD2 PHE A  84 "
       pdb=" HD2 PHE A  84 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C5    C B 252 "
       pdb=" H5    C B 252 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C2    A B 139 "
       pdb=" H2    A B 139 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C6    C B 253 "
       pdb=" H6    C B 253 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  ... (remaining 14947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.22: 23959
        3.22 -     6.44: 2518
        6.44 -     9.66: 263
        9.66 -    12.88: 23
       12.88 -    16.10: 2
  Bond angle restraints: 26765
  Sorted by residual:
  angle pdb=" O3'   G B 329 "
        pdb=" C3'   G B 329 "
        pdb=" C2'   G B 329 "
      ideal   model   delta    sigma   weight residual
     109.50  125.60  -16.10 1.50e+00 4.44e-01 1.15e+02
  angle pdb=" O3'   G B 133 "
        pdb=" C3'   G B 133 "
        pdb=" C2'   G B 133 "
      ideal   model   delta    sigma   weight residual
     109.50  123.51  -14.01 1.50e+00 4.44e-01 8.73e+01
  angle pdb=" O4'   G B 137 "
        pdb=" C1'   G B 137 "
        pdb=" C2'   G B 137 "
      ideal   model   delta    sigma   weight residual
     107.60   98.64    8.96 1.00e+00 1.00e+00 8.03e+01
  angle pdb=" C4'   G B 175 "
        pdb=" O4'   G B 175 "
        pdb=" C1'   G B 175 "
      ideal   model   delta    sigma   weight residual
     109.90  101.17    8.73 1.00e+00 1.00e+00 7.63e+01
  angle pdb=" O3'   A B 173 "
        pdb=" C3'   A B 173 "
        pdb=" C2'   A B 173 "
      ideal   model   delta    sigma   weight residual
     109.50  121.88  -12.38 1.50e+00 4.44e-01 6.81e+01
  ... (remaining 26760 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.99: 6205
       35.99 -    71.98: 1166
       71.98 -   107.97: 169
      107.97 -   143.96: 24
      143.96 -   179.95: 42
  Dihedral angle restraints: 7606
    sinusoidal: 7232
      harmonic: 374
  Sorted by residual:
  dihedral pdb=" C5'   A B 139 "
           pdb=" C4'   A B 139 "
           pdb=" C3'   A B 139 "
           pdb=" O3'   A B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   61.67   85.33     1      8.00e+00 1.56e-02 1.38e+02
  dihedral pdb=" C5'   C B 122 "
           pdb=" C4'   C B 122 "
           pdb=" C3'   C B 122 "
           pdb=" O3'   C B 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   67.95   79.05     1      8.00e+00 1.56e-02 1.22e+02
  dihedral pdb=" C5'   A B 351 "
           pdb=" C4'   A B 351 "
           pdb=" C3'   A B 351 "
           pdb=" O3'   A B 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   68.43   78.57     1      8.00e+00 1.56e-02 1.20e+02
  ... (remaining 7603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.204: 1885
       0.204 -    0.408: 90
       0.408 -    0.611: 23
       0.611 -    0.815: 4
       0.815 -    1.019: 1
  Chirality restraints: 2003
  Sorted by residual:
  chirality pdb=" P     C B 145 "
            pdb=" OP1   C B 145 "
            pdb=" OP2   C B 145 "
            pdb=" O5'   C B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -1.39    1.02 2.00e-01 2.50e+01 2.59e+01
  chirality pdb=" C3'   G B 329 "
            pdb=" C4'   G B 329 "
            pdb=" O3'   G B 329 "
            pdb=" C2'   G B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -1.94   -0.80 2.00e-01 2.50e+01 1.60e+01
  chirality pdb=" C3'   A B 192 "
            pdb=" C4'   A B 192 "
            pdb=" O3'   A B 192 "
            pdb=" C2'   A B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.03   -0.72 2.00e-01 2.50e+01 1.29e+01
  ... (remaining 2000 not shown)

  Planarity restraints: 960
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 145 "    0.971 2.00e-02 2.50e+03   3.80e-01 3.97e+03
        pdb=" N1    C B 145 "   -0.066 2.00e-02 2.50e+03
        pdb=" C2    C B 145 "   -0.167 2.00e-02 2.50e+03
        pdb=" O2    C B 145 "   -0.557 2.00e-02 2.50e+03
        pdb=" N3    C B 145 "    0.079 2.00e-02 2.50e+03
        pdb=" C4    C B 145 "    0.134 2.00e-02 2.50e+03
        pdb=" N4    C B 145 "    0.343 2.00e-02 2.50e+03
        pdb=" C5    C B 145 "   -0.106 2.00e-02 2.50e+03
        pdb=" C6    C B 145 "   -0.216 2.00e-02 2.50e+03
        pdb=" H5    C B 145 "   -0.120 2.00e-02 2.50e+03
        pdb=" H6    C B 145 "   -0.295 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 336 "    0.672 2.00e-02 2.50e+03   2.38e-01 1.98e+03
        pdb=" N9    G B 336 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8    G B 336 "   -0.141 2.00e-02 2.50e+03
        pdb=" N7    G B 336 "   -0.172 2.00e-02 2.50e+03
        pdb=" C5    G B 336 "   -0.097 2.00e-02 2.50e+03
        pdb=" C6    G B 336 "    0.076 2.00e-02 2.50e+03
        pdb=" O6    G B 336 "    0.282 2.00e-02 2.50e+03
        pdb=" N1    G B 336 "    0.044 2.00e-02 2.50e+03
        pdb=" C2    G B 336 "   -0.167 2.00e-02 2.50e+03
        pdb=" N2    G B 336 "   -0.129 2.00e-02 2.50e+03
        pdb=" N3    G B 336 "   -0.246 2.00e-02 2.50e+03
        pdb=" C4    G B 336 "   -0.187 2.00e-02 2.50e+03
        pdb=" H8    G B 336 "   -0.121 2.00e-02 2.50e+03
        pdb=" H1    G B 336 "    0.197 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 144 "    0.603 2.00e-02 2.50e+03   2.26e-01 1.78e+03
        pdb=" N9    G B 144 "    0.017 2.00e-02 2.50e+03
        pdb=" C8    G B 144 "   -0.192 2.00e-02 2.50e+03
        pdb=" N7    G B 144 "   -0.149 2.00e-02 2.50e+03
        pdb=" C5    G B 144 "   -0.042 2.00e-02 2.50e+03
        pdb=" C6    G B 144 "    0.119 2.00e-02 2.50e+03
        pdb=" O6    G B 144 "    0.350 2.00e-02 2.50e+03
        pdb=" N1    G B 144 "    0.061 2.00e-02 2.50e+03
        pdb=" C2    G B 144 "   -0.084 2.00e-02 2.50e+03
        pdb=" N2    G B 144 "   -0.250 2.00e-02 2.50e+03
        pdb=" N3    G B 144 "   -0.082 2.00e-02 2.50e+03
        pdb=" C4    G B 144 "   -0.078 2.00e-02 2.50e+03
        pdb=" H8    G B 144 "   -0.258 2.00e-02 2.50e+03
        pdb=" H1    G B 144 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 957 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 790
        2.08 -     2.71: 14734
        2.71 -     3.34: 35932
        3.34 -     3.97: 54135
        3.97 -     4.60: 74342
  Nonbonded interactions: 179933
  Sorted by model distance:
  nonbonded pdb="HO2'   C B 343 "
            pdb=" H3'   A B 344 "
     model   vdw
     1.453 2.270
  nonbonded pdb="HO2'   A B 181 "
            pdb=" OP2   A B 182 "
     model   vdw
     1.497 2.450
  nonbonded pdb=" OP1   C B 145 "
            pdb="HO2'   G B 147 "
     model   vdw
     1.562 2.450
  nonbonded pdb="HO2'   A B 193 "
            pdb=" OP1   G B 194 "
     model   vdw
     1.565 2.450
  nonbonded pdb="HO2'   G B 165 "
            pdb=" OP1   A B 166 "
     model   vdw
     1.566 2.450
  ... (remaining 179928 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.89
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.920
  Find NCS groups from input model:        0.040
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5949
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      :  0.015   0.063   9928  Z= 0.869
  Angle     :  2.219  16.101  15291  Z= 1.426
  Chirality :  0.120   1.019   2003
  Planarity :  0.058   0.386    538
  Dihedral  : 31.483 179.953   6256
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  6.36 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.20 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.76), residues: 110
  helix: -3.09 (0.62), residues: 37
  sheet:  1.09 (1.36), residues: 12
  loop : -1.55 (0.83), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  75 
 PHE   0.043   0.012   PHE A  84 
 TRP   0.039   0.021   TRP A 108 
 HIS   0.007   0.003   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.01482 ( 9928)
  covalent geometry    : angle       2.21925 (15291)
  hydrogen bonds       : bond        0.12440 (  287)
  hydrogen bonds       : angle       8.43930 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.3718
  time to fit residues: 10.4511
Evaluate side-chains
  17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.123154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.107998 restraints weight = 122539.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 1.03
r_work: 0.3988 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9928  Z= 0.222
  Angle     :  1.029   9.907  15291  Z= 0.540
  Chirality :  0.052   0.323   2003
  Planarity :  0.006   0.036    538
  Dihedral  : 30.554 179.841   6011
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  4.55 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.22 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.75), residues: 110
  helix: -2.76 (0.53), residues: 54
  sheet:  0.12 (1.06), residues: 19
  loop : -1.24 (1.18), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 109 
 PHE   0.014   0.002   PHE A  84 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.003   0.002   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9928)
  covalent geometry    : angle       1.02856 (15291)
  hydrogen bonds       : bond        0.08362 (  287)
  hydrogen bonds       : angle       3.10426 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 18
  average time/residue: 0.4019
  time to fit residues: 8.5089
Evaluate side-chains
  13 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0010
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    1.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.119952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.105234 restraints weight = 114809.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 1.60
r_work: 0.3904 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9928  Z= 0.235
  Angle     :  0.889  10.149  15291  Z= 0.466
  Chirality :  0.047   0.317   2003
  Planarity :  0.007   0.042    538
  Dihedral  : 30.391 179.805   6011
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 21.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 17.35 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.74), residues: 110
  helix: -2.26 (0.60), residues: 54
  sheet: -0.83 (1.03), residues: 19
  loop : -1.33 (1.09), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  37 
 PHE   0.016   0.002   PHE A  19 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.008   0.003   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 9928)
  covalent geometry    : angle       0.88860 (15291)
  hydrogen bonds       : bond        0.08820 (  287)
  hydrogen bonds       : angle       3.03950 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 15
  average time/residue: 0.3691
  time to fit residues: 6.6761
Evaluate side-chains
  15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.118272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.103771 restraints weight = 117397.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 2.00
r_work: 0.3857 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6583
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   9928  Z= 0.367
  Angle     :  0.985  10.309  15291  Z= 0.500
  Chirality :  0.051   0.372   2003
  Planarity :  0.007   0.050    538
  Dihedral  : 30.656 178.768   6011
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 31.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.29 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.60 (0.69), residues: 110
  helix: -2.99 (0.51), residues: 54
  sheet: -0.95 (1.02), residues: 19
  loop : -1.79 (1.06), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  37 
 PHE   0.010   0.002   PHE A  84 
 TRP   0.003   0.002   TRP A 108 
 HIS   0.007   0.002   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 9928)
  covalent geometry    : angle       0.98472 (15291)
  hydrogen bonds       : bond        0.11174 (  287)
  hydrogen bonds       : angle       3.47945 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8377 (mtp) cc_final: 0.7923 (mtp)
REVERT: A  108 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.7664 (m-10)
  outliers start: 4
  outliers final: 2
  residues processed: 17
  average time/residue: 0.2684
  time to fit residues: 5.5444
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 13
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  108 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.119396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.104910 restraints weight = 117447.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 1.49
r_work: 0.3895 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9928  Z= 0.247
  Angle     :  0.843   9.506  15291  Z= 0.435
  Chirality :  0.044   0.313   2003
  Planarity :  0.006   0.036    538
  Dihedral  : 30.428 179.569   6011
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.64 %
    Favored  : 86.36 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.33 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.26 (0.71), residues: 110
  helix: -2.72 (0.55), residues: 54
  sheet: -0.52 (1.05), residues: 19
  loop : -1.78 (1.05), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  37 
 PHE   0.011   0.002   PHE A  84 
 TRP   0.003   0.002   TRP A 108 
 HIS   0.004   0.002   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9928)
  covalent geometry    : angle       0.84291 (15291)
  hydrogen bonds       : bond        0.08387 (  287)
  hydrogen bonds       : angle       3.06944 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7970 (tp30) cc_final: 0.7204 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 16
  average time/residue: 0.3267
  time to fit residues: 6.3226
Evaluate side-chains
  15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.118072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.103780 restraints weight = 115780.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 1.73
r_work: 0.3865 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.5625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9928  Z= 0.340
  Angle     :  0.935   9.965  15291  Z= 0.476
  Chirality :  0.049   0.337   2003
  Planarity :  0.007   0.044    538
  Dihedral  : 30.619 178.793   6011
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 30.51
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 14.55 %
    Favored  : 84.55 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.37 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.92 (0.67), residues: 110
  helix: -3.25 (0.48), residues: 54
  sheet: -0.72 (1.05), residues: 19
  loop : -2.20 (1.02), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  37 
 PHE   0.009   0.002   PHE A  84 
 TRP   0.002   0.001   TRP A 108 
 HIS   0.005   0.002   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 9928)
  covalent geometry    : angle       0.93487 (15291)
  hydrogen bonds       : bond        0.10618 (  287)
  hydrogen bonds       : angle       3.33872 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8187 (mtp) cc_final: 0.7722 (mtp)
REVERT: A  105 GLU cc_start: 0.8033 (tp30) cc_final: 0.7232 (mm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 20
  average time/residue: 0.3402
  time to fit residues: 8.1475
Evaluate side-chains
  20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.118774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.104842 restraints weight = 117060.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 1.53
r_work: 0.3879 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.5943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9928  Z= 0.267
  Angle     :  0.845   9.261  15291  Z= 0.434
  Chirality :  0.045   0.311   2003
  Planarity :  0.006   0.039    538
  Dihedral  : 30.447 179.530   6011
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 10.91 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.39 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.69 (0.70), residues: 110
  helix: -3.14 (0.50), residues: 52
  sheet: -0.49 (1.14), residues: 19
  loop : -2.14 (1.02), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  37 
 PHE   0.009   0.002   PHE A  84 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.005   0.002   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9928)
  covalent geometry    : angle       0.84472 (15291)
  hydrogen bonds       : bond        0.08681 (  287)
  hydrogen bonds       : angle       3.10757 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8129 (mtp) cc_final: 0.7681 (mtp)
REVERT: A  105 GLU cc_start: 0.7969 (tp30) cc_final: 0.7188 (mm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 20
  average time/residue: 0.3651
  time to fit residues: 8.7105
Evaluate side-chains
  19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.2782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.119526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.105408 restraints weight = 116150.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 1.49
r_work: 0.3917 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.6425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9928  Z= 0.195
  Angle     :  0.758   8.831  15291  Z= 0.393
  Chirality :  0.040   0.291   2003
  Planarity :  0.006   0.047    538
  Dihedral  : 30.199 177.662   6011
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  5.45 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 20.41 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.72), residues: 110
  helix: -2.65 (0.56), residues: 46
  sheet: -0.74 (1.16), residues: 21
  loop : -2.35 (0.96), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 109 
 PHE   0.007   0.002   PHE A  84 
 TRP   0.001   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9928)
  covalent geometry    : angle       0.75761 (15291)
  hydrogen bonds       : bond        0.07501 (  287)
  hydrogen bonds       : angle       2.88194 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8194 (mtp) cc_final: 0.7785 (mtp)
REVERT: A  105 GLU cc_start: 0.7978 (tp30) cc_final: 0.7206 (mm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.3150
  time to fit residues: 7.3152
Evaluate side-chains
  17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.119902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.105331 restraints weight = 117044.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 1.62
r_work: 0.3905 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9928  Z= 0.184
  Angle     :  0.741   8.743  15291  Z= 0.383
  Chirality :  0.039   0.310   2003
  Planarity :  0.006   0.038    538
  Dihedral  : 30.097 178.776   6011
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  4.55 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.37 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.75), residues: 110
  helix: -2.17 (0.65), residues: 44
  sheet: -0.95 (1.13), residues: 21
  loop : -1.94 (0.95), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 109 
 PHE   0.010   0.002   PHE A  19 
 TRP   0.002   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9928)
  covalent geometry    : angle       0.74140 (15291)
  hydrogen bonds       : bond        0.07244 (  287)
  hydrogen bonds       : angle       2.75115 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 GLU cc_start: 0.7776 (tp30) cc_final: 0.7524 (tp30)
REVERT: A  105 GLU cc_start: 0.7957 (tp30) cc_final: 0.7138 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.3472
  time to fit residues: 7.7123
Evaluate side-chains
  16 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.2988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.118130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.103419 restraints weight = 117454.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 1.63
r_work: 0.3856 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
moved from start:          0.6784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9928  Z= 0.304
  Angle     :  0.857   8.770  15291  Z= 0.436
  Chirality :  0.045   0.325   2003
  Planarity :  0.007   0.050    538
  Dihedral  : 30.290 179.440   6011
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 10.91 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 20.41 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.64 (0.71), residues: 110
  helix: -2.68 (0.59), residues: 46
  sheet: -1.00 (1.12), residues: 21
  loop : -2.65 (0.92), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  73 
 PHE   0.011   0.002   PHE A  84 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.004   0.002   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 9928)
  covalent geometry    : angle       0.85666 (15291)
  hydrogen bonds       : bond        0.09449 (  287)
  hydrogen bonds       : angle       3.09217 (  533)

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

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

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  220 Ramachandran restraints generated.
    110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.7751 (tp30) cc_final: 0.7518 (tp30)
REVERT: A  105 GLU cc_start: 0.8057 (tp30) cc_final: 0.7242 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 17
  average time/residue: 0.3170
  time to fit residues: 6.4526
Evaluate side-chains
  18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.118190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.103640 restraints weight = 116337.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 1.72
r_work: 0.3861 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.6923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9928  Z= 0.289
  Angle     :  0.832   8.967  15291  Z= 0.425
  Chirality :  0.044   0.319   2003
  Planarity :  0.007   0.068    538
  Dihedral  : 30.281 178.994   6011
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 22.24
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 11.82 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.37 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.82 (0.70), residues: 110
  helix: -2.95 (0.54), residues: 46
  sheet: -0.85 (1.12), residues: 21
  loop : -2.75 (0.92), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 PHE   0.009   0.002   PHE A  84 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.004   0.002   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 9928)
  covalent geometry    : angle       0.83215 (15291)
  hydrogen bonds       : bond        0.08899 (  287)
  hydrogen bonds       : angle       3.07571 (  533)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5130.59 seconds
wall clock time: 87 minutes 29.21 seconds (5249.21 seconds total)