Starting phenix.real_space_refine
on Sat Apr  4 22:24:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u5r_63881/04_2026/9u5r_63881.map"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   1.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      75      5.49       5
     S      15      5.16       5
     C    2692      2.51       5
     N     816      2.21       5
     O    1145      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4743
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "O"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1391
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "P"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 973
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "Q"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 792
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "R"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1587
          Classifications: {'RNA': 75}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 8, 'rna3p': 66}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.18, per 1000 atoms: 0.25
  Number of scatterers: 4743
  At special positions: 0
  Unit cell: (82.56, 88.32, 109.44, 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      15     16.00
     P      75     15.00
     O    1145      8.00
     N     816      7.00
     C    2692      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS P  24 " - pdb=" SG  CYS P  98 " distance=2.99

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 250.2 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  734

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 8 sheets defined
      8.9% alpha, 44.2% beta
      26 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'O' and resid 3 through 14
    Processing helix  chain 'O' and resid 38 through 42
    Processing helix  chain 'O' and resid 86 through 90
      removed outlier: 3.882A  pdb=" N   ILE O  90 " --> pdb=" O   ARG O  87 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 89 through 93
      removed outlier: 3.791A  pdb=" N   THR P  93 " --> pdb=" O   ALA P  90 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 26 through 30
      removed outlier: 3.837A  pdb=" N   ASP Q  29 " --> pdb=" O   LYS Q  26 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 78 through 82
      removed outlier: 4.019A  pdb=" N   GLU Q  82 " --> pdb=" O   ALA Q  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 15 through 20
      removed outlier: 6.956A  pdb=" N   VAL O  34 " --> pdb=" O   ILE O  30 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE O  68 " --> pdb=" O   ASP O  64 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU O  70 " --> pdb=" O   LEU O  62 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU O  62 " --> pdb=" O   LEU O  70 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LEU O  72 " --> pdb=" O   TYR O  60 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TYR O  60 " --> pdb=" O   LEU O  72 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   VAL O  74 " --> pdb=" O   ASP O  58 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ASP O  58 " --> pdb=" O   VAL O  74 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   THR O  76 " --> pdb=" O   VAL O  56 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL O  56 " --> pdb=" O   THR O  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 119 through 120
      removed outlier: 3.748A  pdb=" N   THR O 119 " --> pdb=" O   ARG O 136 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   ALA O 171 " --> pdb=" O   HIS O 160 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   HIS O 160 " --> pdb=" O   ALA O 171 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   ILE O 156 " --> pdb=" O   ALA O 152 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ALA O 152 " --> pdb=" O   ILE O 156 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY O 158 " --> pdb=" O   LEU O 150 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   SER O 105 " --> pdb=" O   THR O 109 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR O 109 " --> pdb=" O   SER O 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 123 through 126
      removed outlier: 3.752A  pdb=" N   ILE O 124 " --> pdb=" O   THR O 131 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR O 131 " --> pdb=" O   ILE O 124 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 5 through 10
    Processing sheet with id=AA5, first strand: chain 'P' and resid 12 through 14
      removed outlier: 3.660A  pdb=" N   GLY P  12 " --> pdb=" O   THR P 123 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR P 125 " --> pdb=" O   GLY P  12 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   MET P  36 " --> pdb=" O   VAL P  52 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL P  52 " --> pdb=" O   MET P  36 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP P  38 " --> pdb=" O   VAL P  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5
    Processing sheet with id=AA7, first strand: chain 'Q' and resid 9 through 11
      removed outlier: 3.682A  pdb=" N   THR Q 104 " --> pdb=" O   VAL Q  10 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR Q  31 " --> pdb=" O   TRP Q  90 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TRP Q  34 " --> pdb=" O   VAL Q  46 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 9 through 11
      removed outlier: 3.682A  pdb=" N   THR Q 104 " --> pdb=" O   VAL Q  10 " (cutoff:3.500A)

    122 hydrogen bonds defined for protein.
    297 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      67 hydrogen bonds
      126 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 0.76

  Time building geometry restraints manager: 0.54 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: 1217
        1.34 -     1.46: 1487
        1.46 -     1.58: 2113
        1.58 -     1.70: 148
        1.70 -     1.82: 22
  Bond restraints: 4987
  Sorted by residual:
  bond pdb=" C   VAL Q   3 "
       pdb=" O   VAL Q   3 "
    ideal  model  delta    sigma   weight residual
    1.236  1.275 -0.039 1.04e-02 9.25e+03 1.41e+01
  bond pdb=" CA  PRO Q   7 "
       pdb=" C   PRO Q   7 "
    ideal  model  delta    sigma   weight residual
    1.514  1.495  0.019 5.50e-03 3.31e+04 1.25e+01
  bond pdb=" C   TYR Q   2 "
       pdb=" O   TYR Q   2 "
    ideal  model  delta    sigma   weight residual
    1.234  1.278 -0.044 1.27e-02 6.20e+03 1.19e+01
  bond pdb=" CA  SER Q  11 "
       pdb=" CB  SER Q  11 "
    ideal  model  delta    sigma   weight residual
    1.534  1.482  0.052 1.76e-02 3.23e+03 8.62e+00
  bond pdb=" N   GLN P   8 "
       pdb=" CA  GLN P   8 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.18e-02 7.18e+03 8.26e+00
  ... (remaining 4982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 6813
        2.08 -     4.15: 262
        4.15 -     6.23: 27
        6.23 -     8.31: 2
        8.31 -    10.39: 2
  Bond angle restraints: 7106
  Sorted by residual:
  angle pdb=" N   TYR P  97 "
        pdb=" CA  TYR P  97 "
        pdb=" C   TYR P  97 "
      ideal   model   delta    sigma   weight residual
     110.42  116.36   -5.94 1.55e+00 4.16e-01 1.47e+01
  angle pdb=" N   TYR P  96 "
        pdb=" CA  TYR P  96 "
        pdb=" C   TYR P  96 "
      ideal   model   delta    sigma   weight residual
     108.90  114.59   -5.69 1.63e+00 3.76e-01 1.22e+01
  angle pdb=" CB  MET Q  80 "
        pdb=" CG  MET Q  80 "
        pdb=" SD  MET Q  80 "
      ideal   model   delta    sigma   weight residual
     112.70  123.09  -10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N   TYR P  97 "
        pdb=" CA  TYR P  97 "
        pdb=" CB  TYR P  97 "
      ideal   model   delta    sigma   weight residual
     110.56  105.24    5.32 1.56e+00 4.11e-01 1.16e+01
  angle pdb=" C   VAL Q   3 "
        pdb=" N   LEU Q   4 "
        pdb=" CA  LEU Q   4 "
      ideal   model   delta    sigma   weight residual
     122.99  118.24    4.75 1.41e+00 5.03e-01 1.13e+01
  ... (remaining 7101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.25: 2718
       26.25 -    52.49: 217
       52.49 -    78.74: 133
       78.74 -   104.99: 5
      104.99 -   131.24: 1
  Dihedral angle restraints: 3074
    sinusoidal: 1910
      harmonic: 1164
  Sorted by residual:
  dihedral pdb=" O4'   A R  36 "
           pdb=" C1'   A R  36 "
           pdb=" N9    A R  36 "
           pdb=" C4    A R  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -178.10   72.10     1      1.70e+01 3.46e-03 2.30e+01
  dihedral pdb=" CB  CYS P  24 "
           pdb=" SG  CYS P  24 "
           pdb=" SG  CYS P  98 "
           pdb=" CB  CYS P  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.89   36.11     1      1.00e+01 1.00e-02 1.84e+01
  dihedral pdb=" C4'   U R  14 "
           pdb=" C3'   U R  14 "
           pdb=" O3'   U R  14 "
           pdb=" P     G R  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   88.76  131.24     1      3.50e+01 8.16e-04 1.30e+01
  ... (remaining 3071 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 703
       0.107 -    0.214: 141
       0.214 -    0.321: 12
       0.321 -    0.428: 2
       0.428 -    0.534: 2
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" P     C R  25 "
            pdb=" OP1   C R  25 "
            pdb=" OP2   C R  25 "
            pdb=" O5'   C R  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 7.14e+00
  chirality pdb=" P     A R  32 "
            pdb=" OP1   A R  32 "
            pdb=" OP2   A R  32 "
            pdb=" O5'   A R  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.23e+00
  chirality pdb=" P     G R   1 "
            pdb=" OP1   G R   1 "
            pdb=" OP2   G R   1 "
            pdb=" O5'   G R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.83   -0.42 2.00e-01 2.50e+01 4.48e+00
  ... (remaining 857 not shown)

  Planarity restraints: 635
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE O  37 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.30e+00
        pdb=" N   PRO O  38 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO O  38 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO O  38 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG O  79 "    0.161 9.50e-02 1.11e+02   7.20e-02 3.19e+00
        pdb=" NE  ARG O  79 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG O  79 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG O  79 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG O  79 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU P   7 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   LEU P   7 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LEU P   7 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLN P   8 "    0.009 2.00e-02 2.50e+03
  ... (remaining 632 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 39
        2.54 -     3.13: 3445
        3.13 -     3.72: 7896
        3.72 -     4.31: 10450
        4.31 -     4.90: 16042
  Nonbonded interactions: 37872
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP O  64 "
            pdb=" CD  PRO O  65 "
     model   vdw
     1.945 3.440
  nonbonded pdb=" O   ASP O  93 "
            pdb=" OD1 ASP O  93 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG1 THR O  26 "
            pdb=" OG  SER O 105 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG  SER P  19 "
            pdb=" OE1 GLN P  84 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD2 ASP P  75 "
            pdb=" NZ  LYS P  78 "
     model   vdw
     2.257 3.120
  ... (remaining 37867 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=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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.870
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4984
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   0.958   4988  Z= 0.779
  Angle     :  0.912  10.960   7108  Z= 0.507
  Chirality :  0.081   0.534    860
  Planarity :  0.005   0.072    635
  Dihedral  : 21.108 131.235   2337
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.22 %
    Favored  : 74.78 %
  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: -0.34 (0.44), residues: 408
  helix:  0.40 (1.53), residues: 12
  sheet:  0.04 (0.42), residues: 171
  loop : -0.40 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG O  84 
 TYR   0.021   0.002   TYR O  60 
 PHE   0.008   0.001   PHE O 178 
 TRP   0.009   0.002   TRP Q  90 
 HIS   0.005   0.001   HIS O  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 4987)
  covalent geometry    : angle       0.90261 ( 7106)
  SS BOND              : bond        0.95774 (    1)
  SS BOND              : angle       7.80458 (    2)
  hydrogen bonds       : bond        0.14833 (  186)
  hydrogen bonds       : angle       5.96863 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: O   13 LYS cc_start: 0.7342 (mttt) cc_final: 0.6726 (mttt)
REVERT: O   14 ASN cc_start: 0.7351 (m110) cc_final: 0.6707 (t0)
REVERT: O  134 MET cc_start: 0.7172 (mtm) cc_final: 0.6959 (ptt)
REVERT: P  112 SER cc_start: 0.7727 (m) cc_final: 0.7351 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0906
  time to fit residues: 4.6077
Evaluate side-chains
  39 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0170
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
O  80 ASN
O 110 ASN
O 145 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.212983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.190414 restraints weight = 8475.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.194302 restraints weight = 4532.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.196898 restraints weight = 2793.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.198670 restraints weight = 1914.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.199879 restraints weight = 1428.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5344
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4988  Z= 0.194
  Angle     :  0.676   7.126   7108  Z= 0.350
  Chirality :  0.040   0.221    860
  Planarity :  0.006   0.063    635
  Dihedral  : 20.800 131.106   1625
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 21.45 %
    Favored  : 74.49 %
  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: -0.38 (0.42), residues: 408
  helix:  1.92 (1.52), residues: 12
  sheet:  0.37 (0.45), residues: 145
  loop : -0.75 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  74 
 TYR   0.018   0.002   TYR Q  31 
 PHE   0.019   0.002   PHE O  83 
 TRP   0.012   0.002   TRP P 109 
 HIS   0.006   0.002   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 4987)
  covalent geometry    : angle       0.67338 ( 7106)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       3.60480 (    2)
  hydrogen bonds       : bond        0.05292 (  186)
  hydrogen bonds       : angle       4.70238 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.079 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7456 (mmmm) cc_final: 0.7059 (mtmt)
REVERT: P   72 ILE cc_start: 0.3922 (OUTLIER) cc_final: 0.3486 (pt)
  outliers start: 14
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0744
  time to fit residues: 5.6215
Evaluate side-chains
  55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue   72 ILE
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   55 SER
Chi-restraints excluded: chain Q residue   94 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
O  42 GLN
P  84 GLN
Q   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.206957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.185101 restraints weight = 8584.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.188564 restraints weight = 4802.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.190924 restraints weight = 3064.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.192499 restraints weight = 2157.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.193570 restraints weight = 1652.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5501
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4988  Z= 0.196
  Angle     :  0.703   9.014   7108  Z= 0.362
  Chirality :  0.041   0.225    860
  Planarity :  0.006   0.056    635
  Dihedral  : 20.684 132.360   1625
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 20.58 %
    Favored  : 73.91 %
  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: -0.36 (0.42), residues: 408
  helix:  2.44 (1.58), residues: 12
  sheet:  0.49 (0.42), residues: 160
  loop : -0.93 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  40 
 TYR   0.017   0.002   TYR P  97 
 PHE   0.015   0.002   PHE O  83 
 TRP   0.014   0.003   TRP Q  90 
 HIS   0.005   0.002   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4987)
  covalent geometry    : angle       0.70148 ( 7106)
  SS BOND              : bond        0.00832 (    1)
  SS BOND              : angle       2.90157 (    2)
  hydrogen bonds       : bond        0.05644 (  186)
  hydrogen bonds       : angle       4.87746 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.130 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7172 (mmmm) cc_final: 0.6675 (mtpt)
REVERT: O   87 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.4492 (mtp180)
REVERT: P   61 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6448 (m-10)
  outliers start: 19
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0837
  time to fit residues: 6.1057
Evaluate side-chains
  55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain O residue   87 ARG
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  114 GLU
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain O residue  159 ILE
Chi-restraints excluded: chain P residue   20 LEU
Chi-restraints excluded: chain P residue   61 TYR
Chi-restraints excluded: chain P residue  115 MET
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   55 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
P  84 GLN
** Q  88 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 = 0.4577 r_free = 0.4577 target = 0.205904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.184346 restraints weight = 8620.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.187883 restraints weight = 4791.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.190263 restraints weight = 3015.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.191888 restraints weight = 2101.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.192999 restraints weight = 1589.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5516
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4988  Z= 0.167
  Angle     :  0.647   8.723   7108  Z= 0.333
  Chirality :  0.040   0.237    860
  Planarity :  0.005   0.054    635
  Dihedral  : 20.669 132.886   1625
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 22.03 %
    Favored  : 72.17 %
  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: -0.44 (0.42), residues: 408
  helix:  2.49 (1.61), residues: 12
  sheet:  0.29 (0.40), residues: 166
  loop : -0.88 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O 133 
 TYR   0.013   0.002   TYR P  62 
 PHE   0.011   0.002   PHE O  83 
 TRP   0.012   0.002   TRP Q  90 
 HIS   0.003   0.001   HIS O 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4987)
  covalent geometry    : angle       0.64588 ( 7106)
  SS BOND              : bond        0.00910 (    1)
  SS BOND              : angle       1.87541 (    2)
  hydrogen bonds       : bond        0.05181 (  186)
  hydrogen bonds       : angle       4.65540 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.105 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7248 (mmmm) cc_final: 0.6698 (mtpt)
  outliers start: 20
  outliers final: 16
  residues processed: 56
  average time/residue: 0.0879
  time to fit residues: 6.0955
Evaluate side-chains
  59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  114 GLU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue  115 MET
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   71 THR
Chi-restraints excluded: chain Q residue   94 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** Q  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.207485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.185644 restraints weight = 8572.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.189412 restraints weight = 4602.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.191939 restraints weight = 2821.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.193622 restraints weight = 1916.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.194753 restraints weight = 1418.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5503
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4988  Z= 0.136
  Angle     :  0.595   8.239   7108  Z= 0.307
  Chirality :  0.038   0.235    860
  Planarity :  0.004   0.051    635
  Dihedral  : 20.559 133.206   1625
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 25.22 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.42), residues: 408
  helix:  2.60 (1.59), residues: 12
  sheet:  0.38 (0.41), residues: 166
  loop : -0.87 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q  60 
 TYR   0.011   0.002   TYR P  82 
 PHE   0.008   0.001   PHE O  25 
 TRP   0.012   0.002   TRP Q  90 
 HIS   0.004   0.002   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4987)
  covalent geometry    : angle       0.59470 ( 7106)
  SS BOND              : bond        0.01009 (    1)
  SS BOND              : angle       1.47451 (    2)
  hydrogen bonds       : bond        0.04746 (  186)
  hydrogen bonds       : angle       4.51279 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.088 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7373 (mttt) cc_final: 0.7003 (mttp)
  outliers start: 15
  outliers final: 12
  residues processed: 54
  average time/residue: 0.0793
  time to fit residues: 5.4813
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0000
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
P  84 GLN
** Q  88 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 = 0.4589 r_free = 0.4589 target = 0.206877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.185251 restraints weight = 8506.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.188943 restraints weight = 4603.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.191382 restraints weight = 2832.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.192983 restraints weight = 1940.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.194062 restraints weight = 1453.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5514
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4988  Z= 0.134
  Angle     :  0.597   8.691   7108  Z= 0.308
  Chirality :  0.039   0.237    860
  Planarity :  0.004   0.049    635
  Dihedral  : 20.534 133.292   1625
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 22.90 %
    Favored  : 72.17 %
  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: -0.25 (0.42), residues: 408
  helix:  2.72 (1.60), residues: 12
  sheet:  0.66 (0.42), residues: 152
  loop : -0.89 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  55 
 TYR   0.012   0.002   TYR P  82 
 PHE   0.008   0.001   PHE O  25 
 TRP   0.012   0.002   TRP Q  90 
 HIS   0.003   0.001   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4987)
  covalent geometry    : angle       0.59668 ( 7106)
  SS BOND              : bond        0.00852 (    1)
  SS BOND              : angle       1.35275 (    2)
  hydrogen bonds       : bond        0.04841 (  186)
  hydrogen bonds       : angle       4.46584 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.127 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7381 (mttp) cc_final: 0.7034 (mttp)
REVERT: O  120 MET cc_start: 0.5126 (ppp) cc_final: 0.4751 (ppp)
  outliers start: 17
  outliers final: 15
  residues processed: 53
  average time/residue: 0.0840
  time to fit residues: 5.6301
Evaluate side-chains
  57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
P   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.203155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.181174 restraints weight = 8320.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.184785 restraints weight = 4521.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.187145 restraints weight = 2814.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.188718 restraints weight = 1949.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.189779 restraints weight = 1469.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5633
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4988  Z= 0.213
  Angle     :  0.734  11.122   7108  Z= 0.378
  Chirality :  0.042   0.239    860
  Planarity :  0.005   0.049    635
  Dihedral  : 20.858 132.540   1625
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 22.90 %
    Favored  : 70.72 %
  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: -0.84 (0.41), residues: 408
  helix:  2.50 (1.63), residues: 12
  sheet:  0.06 (0.40), residues: 164
  loop : -1.20 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG O  55 
 TYR   0.022   0.003   TYR O 139 
 PHE   0.012   0.002   PHE O  83 
 TRP   0.015   0.002   TRP Q  90 
 HIS   0.004   0.001   HIS O 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 4987)
  covalent geometry    : angle       0.73317 ( 7106)
  SS BOND              : bond        0.01287 (    1)
  SS BOND              : angle       2.43496 (    2)
  hydrogen bonds       : bond        0.06230 (  186)
  hydrogen bonds       : angle       4.95211 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 43
  time to evaluate  : 0.139 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7437 (mttp) cc_final: 0.7087 (mttp)
REVERT: O  120 MET cc_start: 0.5184 (ppp) cc_final: 0.4948 (ppp)
REVERT: P   61 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6202 (m-10)
REVERT: P  115 MET cc_start: 0.5794 (mmt) cc_final: 0.5576 (mmt)
  outliers start: 22
  outliers final: 18
  residues processed: 56
  average time/residue: 0.0857
  time to fit residues: 6.0869
Evaluate side-chains
  62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain O residue  159 ILE
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   61 TYR
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   71 THR
Chi-restraints excluded: chain Q residue   94 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 24 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0020
   chunk 6 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.3846

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

Flipped N/Q/H residues before XYZ refinement:
P  84 GLN
** Q  88 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 = 0.4603 r_free = 0.4603 target = 0.207940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.185989 restraints weight = 8476.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.189652 restraints weight = 4581.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.192092 restraints weight = 2843.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.193759 restraints weight = 1955.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.194686 restraints weight = 1464.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5544
moved from start:          0.5167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4988  Z= 0.120
  Angle     :  0.604   8.508   7108  Z= 0.308
  Chirality :  0.038   0.234    860
  Planarity :  0.004   0.046    635
  Dihedral  : 20.543 131.491   1625
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.77 %
    Favored  : 71.30 %
  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: -0.59 (0.41), residues: 408
  helix:  3.21 (1.61), residues: 11
  sheet:  0.26 (0.41), residues: 164
  loop : -1.08 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  55 
 TYR   0.011   0.001   TYR P  82 
 PHE   0.007   0.001   PHE O 108 
 TRP   0.011   0.002   TRP Q  90 
 HIS   0.004   0.001   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4987)
  covalent geometry    : angle       0.60401 ( 7106)
  SS BOND              : bond        0.00650 (    1)
  SS BOND              : angle       0.69467 (    2)
  hydrogen bonds       : bond        0.04626 (  186)
  hydrogen bonds       : angle       4.50783 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.127 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7360 (mttp) cc_final: 0.7046 (mttp)
REVERT: O  120 MET cc_start: 0.4970 (ppp) cc_final: 0.4628 (ppp)
  outliers start: 17
  outliers final: 16
  residues processed: 50
  average time/residue: 0.0713
  time to fit residues: 4.6876
Evaluate side-chains
  55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue   80 THR
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   71 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.0000
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0010
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
P  84 GLN
** Q  88 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 = 0.4596 r_free = 0.4596 target = 0.207329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.185711 restraints weight = 8461.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.189180 restraints weight = 4639.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.191506 restraints weight = 2918.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.193086 restraints weight = 2017.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.194141 restraints weight = 1525.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5552
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4988  Z= 0.129
  Angle     :  0.623  12.290   7108  Z= 0.316
  Chirality :  0.038   0.236    860
  Planarity :  0.004   0.047    635
  Dihedral  : 20.526 132.255   1625
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 23.77 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.41), residues: 408
  helix:  3.13 (1.65), residues: 11
  sheet:  0.21 (0.41), residues: 164
  loop : -1.04 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  55 
 TYR   0.011   0.002   TYR O 139 
 PHE   0.008   0.001   PHE O  25 
 TRP   0.013   0.002   TRP Q  90 
 HIS   0.004   0.002   HIS O 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4987)
  covalent geometry    : angle       0.62301 ( 7106)
  SS BOND              : bond        0.00868 (    1)
  SS BOND              : angle       1.30360 (    2)
  hydrogen bonds       : bond        0.04888 (  186)
  hydrogen bonds       : angle       4.44506 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.139 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7329 (mttp) cc_final: 0.7038 (mttp)
REVERT: O  120 MET cc_start: 0.5061 (ppp) cc_final: 0.4743 (ppp)
  outliers start: 18
  outliers final: 17
  residues processed: 49
  average time/residue: 0.0836
  time to fit residues: 5.1964
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue   80 THR
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
P  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.204794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.183040 restraints weight = 8379.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.186618 restraints weight = 4513.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.188980 restraints weight = 2803.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.190590 restraints weight = 1935.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.191631 restraints weight = 1453.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5614
moved from start:          0.5692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4988  Z= 0.179
  Angle     :  0.678  10.369   7108  Z= 0.347
  Chirality :  0.040   0.237    860
  Planarity :  0.005   0.047    635
  Dihedral  : 20.699 131.465   1625
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 24.06 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.41), residues: 408
  helix:  2.40 (1.65), residues: 12
  sheet:  0.21 (0.41), residues: 163
  loop : -1.19 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O  55 
 TYR   0.016   0.002   TYR O 139 
 PHE   0.011   0.002   PHE O  25 
 TRP   0.014   0.002   TRP P  49 
 HIS   0.006   0.002   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4987)
  covalent geometry    : angle       0.67749 ( 7106)
  SS BOND              : bond        0.01125 (    1)
  SS BOND              : angle       1.85035 (    2)
  hydrogen bonds       : bond        0.05605 (  186)
  hydrogen bonds       : angle       4.69538 (  423)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.133 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7384 (mttp) cc_final: 0.7047 (mttp)
REVERT: O  120 MET cc_start: 0.5179 (ppp) cc_final: 0.4901 (ppp)
  outliers start: 17
  outliers final: 16
  residues processed: 48
  average time/residue: 0.0743
  time to fit residues: 4.6438
Evaluate side-chains
  54 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   26 THR
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue   97 VAL
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  118 VAL
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
Chi-restraints excluded: chain P residue   67 LYS
Chi-restraints excluded: chain P residue  120 LYS
Chi-restraints excluded: chain Q residue   17 THR
Chi-restraints excluded: chain Q residue   46 VAL
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0570
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
O  80 ASN
** Q  88 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 = 0.4604 r_free = 0.4604 target = 0.207989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.186635 restraints weight = 8482.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.190134 restraints weight = 4592.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.192494 restraints weight = 2850.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.194051 restraints weight = 1964.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.195076 restraints weight = 1482.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5544
moved from start:          0.5713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4988  Z= 0.121
  Angle     :  0.607   9.149   7108  Z= 0.309
  Chirality :  0.038   0.234    860
  Planarity :  0.004   0.044    635
  Dihedral  : 20.503 131.010   1625
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.77 %
    Favored  : 71.30 %
  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: -0.64 (0.41), residues: 408
  helix:  3.07 (1.65), residues: 11
  sheet:  0.27 (0.41), residues: 162
  loop : -1.13 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  55 
 TYR   0.016   0.002   TYR P  62 
 PHE   0.008   0.001   PHE O  25 
 TRP   0.013   0.002   TRP P  49 
 HIS   0.007   0.002   HIS P  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4987)
  covalent geometry    : angle       0.60677 ( 7106)
  SS BOND              : bond        0.00726 (    1)
  SS BOND              : angle       0.83628 (    2)
  hydrogen bonds       : bond        0.04715 (  186)
  hydrogen bonds       : angle       4.47254 (  423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1006.72 seconds
wall clock time: 18 minutes 3.35 seconds (1083.35 seconds total)