Starting phenix.real_space_refine
on Tue Aug  4 16:23:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u5r_63881/08_2026/9u5r_63881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u5r_63881/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u5r_63881/08_2026/9u5r_63881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u5r_63881/08_2026/9u5r_63881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u5r_63881/08_2026/9u5r_63881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u5r_63881/08_2026/9u5r_63881.cif"
  }
  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-2.2rc3-6140/lib/python3.11/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: 0.94, per 1000 atoms: 0.20
  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: 0.24
  Conformation dependent library (CDL) restraints added in 127.5 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: 0.58
  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: 0.71

  Time building geometry restraints manager: 0.36 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: 6808
        2.08 -     4.15: 267
        4.15 -     6.23: 27
        6.23 -     8.31: 2
        8.31 -    10.39: 2
  Bond angle restraints: 7106
  Sorted by residual:
  angle pdb=" N1    C R  74 "
        pdb=" C2    C R  74 "
        pdb=" O2    C R  74 "
      ideal   model   delta    sigma   weight residual
     118.90  121.23   -2.33 6.00e-01 2.78e+00 1.51e+01
  angle pdb=" C1'   C R  74 "
        pdb=" N1    C R  74 "
        pdb=" C2    C R  74 "
      ideal   model   delta    sigma   weight residual
     118.80  123.03   -4.23 1.10e+00 8.26e-01 1.48e+01
  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
  ... (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: 701
       0.107 -    0.214: 143
       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:             1.670
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.640
  Find NCS groups from input model:        0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5151
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= 0.809
  Angle     :  0.920  10.960   7108  Z= 0.572
  Chirality :  0.083   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/Z
  covalent geometry    : bond        0.00635 /  0.44 ( 4987)
  covalent geometry    : angle       0.91075 /  0.57 ( 7106)
  SS BOND              : bond        0.95774 / 63.85 (    1)
  SS BOND              : angle       7.80458 /  4.13 (    2)
  hydrogen bonds       : bond        0.14833 /  9.13 (  186)
  hydrogen bonds       : angle       5.96863 /  4.61 (  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  : 0.110 
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: 0.0666
  time to fit residues: 3.4718
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  : 0.120 
-------------------------------------------------------------------------------
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...
O  42 GLN
O  80 ASN
O 110 ASN
O 145 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.213817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.192453 restraints weight = 8531.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.195884 restraints weight = 4732.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.198281 restraints weight = 3013.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.199910 restraints weight = 2111.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.201018 restraints weight = 1605.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5474
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4988  Z= 0.189
  Angle     :  0.665   7.416   7108  Z= 0.363
  Chirality :  0.044   0.254    860
  Planarity :  0.006   0.045    635
  Dihedral  : 20.860 133.870   1625
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 19.71 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.42), residues: 408
  helix:  1.49 (1.51), residues: 12
  sheet:  0.17 (0.41), residues: 163
  loop : -0.66 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  74 
 TYR   0.020   0.003   TYR O 139 
 PHE   0.016   0.002   PHE O  83 
 TRP   0.013   0.002   TRP P  38 
 HIS   0.004   0.002   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.19 ( 4987)
  covalent geometry    : angle       0.66193 /  0.36 ( 7106)
  SS BOND              : bond        0.00197 /  0.13 (    1)
  SS BOND              : angle       3.59814 /  2.38 (    2)
  hydrogen bonds       : bond        0.05397 /  3.61 (  186)
  hydrogen bonds       : angle       4.87473 /  3.62 (  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
  61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.115 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7508 (mmmm) cc_final: 0.7140 (mtmt)
  outliers start: 16
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0696
  time to fit residues: 5.0119
Evaluate side-chains
  52 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain P residue   30 THR
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
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:    0.5980
   chunk 3 optimal weight:    0.0270
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4416

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.213124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.193235 restraints weight = 9387.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.196478 restraints weight = 5467.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.198731 restraints weight = 3607.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.200291 restraints weight = 2600.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.201282 restraints weight = 2019.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5492
moved from start:          0.2027

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= 0.132
  Angle     :  0.544   5.758   7108  Z= 0.300
  Chirality :  0.039   0.260    860
  Planarity :  0.005   0.054    635
  Dihedral  : 20.671 134.077   1625
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 22.61 %
    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: -0.13 (0.42), residues: 408
  helix:  2.41 (1.51), residues: 12
  sheet:  0.48 (0.43), residues: 155
  loop : -0.58 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O  87 
 TYR   0.017   0.002   TYR P  96 
 PHE   0.008   0.001   PHE O  83 
 TRP   0.010   0.002   TRP Q  90 
 HIS   0.003   0.001   HIS P  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 ( 4987)
  covalent geometry    : angle       0.54246 /  0.30 ( 7106)
  SS BOND              : bond        0.01193 /  0.80 (    1)
  SS BOND              : angle       2.37799 /  1.44 (    2)
  hydrogen bonds       : bond        0.05045 /  3.42 (  186)
  hydrogen bonds       : angle       4.62195 /  3.45 (  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
  55 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: O   13 LYS cc_start: 0.7497 (mttt) cc_final: 0.7117 (mttt)
REVERT: P   72 ILE cc_start: 0.3652 (OUTLIER) cc_final: 0.3000 (pt)
  outliers start: 12
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0691
  time to fit residues: 4.5769
Evaluate side-chains
  53 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue   72 ILE
Chi-restraints excluded: chain Q residue   17 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0040
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0070
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.3810

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Q   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.212565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.189783 restraints weight = 8994.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.193575 restraints weight = 5031.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.196163 restraints weight = 3207.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.197939 restraints weight = 2255.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.199164 restraints weight = 1713.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5514
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4988  Z= 0.120
  Angle     :  0.522   7.273   7108  Z= 0.287
  Chirality :  0.038   0.266    860
  Planarity :  0.005   0.053    635
  Dihedral  : 20.552 135.518   1625
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.90 %
    Favored  : 73.04 %
  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:  0.03 (0.43), residues: 408
  helix:  2.90 (1.51), residues: 12
  sheet:  0.62 (0.41), residues: 168
  loop : -0.59 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  74 
 TYR   0.021   0.002   TYR P 114 
 PHE   0.009   0.001   PHE O  25 
 TRP   0.010   0.001   TRP Q  90 
 HIS   0.003   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 4987)
  covalent geometry    : angle       0.52095 /  0.29 ( 7106)
  SS BOND              : bond        0.00848 /  0.57 (    1)
  SS BOND              : angle       1.60420 /  1.01 (    2)
  hydrogen bonds       : bond        0.04559 /  3.12 (  186)
  hydrogen bonds       : angle       4.40620 /  3.25 (  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
  53 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.078 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7437 (mttt) cc_final: 0.7142 (mttt)
REVERT: O   22 LYS cc_start: 0.7435 (mmmm) cc_final: 0.7098 (mtmt)
  outliers start: 14
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0698
  time to fit residues: 4.4262
Evaluate side-chains
  48 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 P residue   30 THR
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
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:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0870
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P   5 GLN
Q   6 GLN
** Q  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.212397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.192109 restraints weight = 9278.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.195462 restraints weight = 5246.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.197800 restraints weight = 3373.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.199338 restraints weight = 2383.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.200423 restraints weight = 1819.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5547
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4988  Z= 0.136
  Angle     :  0.545   6.574   7108  Z= 0.297
  Chirality :  0.039   0.266    860
  Planarity :  0.005   0.055    635
  Dihedral  : 20.526 136.166   1625
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.19 %
    Favored  : 73.33 %
  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: -0.08 (0.42), residues: 408
  helix:  3.18 (1.55), residues: 12
  sheet:  0.62 (0.41), residues: 166
  loop : -0.74 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG P  74 
 TYR   0.014   0.002   TYR P  62 
 PHE   0.010   0.001   PHE O  83 
 TRP   0.014   0.002   TRP Q  34 
 HIS   0.004   0.002   HIS P  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.14 ( 4987)
  covalent geometry    : angle       0.54400 /  0.30 ( 7106)
  SS BOND              : bond        0.01091 /  0.73 (    1)
  SS BOND              : angle       1.71079 /  1.08 (    2)
  hydrogen bonds       : bond        0.04935 /  3.36 (  186)
  hydrogen bonds       : angle       4.44256 /  3.23 (  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
  52 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.085 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7438 (mmmm) cc_final: 0.7089 (mtmt)
REVERT: P   52 VAL cc_start: 0.6837 (p) cc_final: 0.6572 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0670
  time to fit residues: 4.1113
Evaluate side-chains
  50 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 P residue   19 SER
Chi-restraints excluded: chain P residue   47 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   chunk 33 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 4 optimal weight:    0.0470
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.2878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P   5 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 = 0.4649 r_free = 0.4649 target = 0.212258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.189430 restraints weight = 9072.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.193230 restraints weight = 5050.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.195839 restraints weight = 3211.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.197619 restraints weight = 2241.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.198812 restraints weight = 1696.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5539
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4988  Z= 0.104
  Angle     :  0.509   7.653   7108  Z= 0.277
  Chirality :  0.037   0.270    860
  Planarity :  0.004   0.054    635
  Dihedral  : 20.508 136.343   1625
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.09 %
    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:  0.05 (0.42), residues: 408
  helix:  2.97 (1.49), residues: 12
  sheet:  0.71 (0.41), residues: 163
  loop : -0.62 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  74 
 TYR   0.016   0.002   TYR P  96 
 PHE   0.010   0.001   PHE P  31 
 TRP   0.010   0.001   TRP Q  90 
 HIS   0.003   0.001   HIS P  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00209 /  0.10 ( 4987)
  covalent geometry    : angle       0.50884 /  0.28 ( 7106)
  SS BOND              : bond        0.00785 /  0.52 (    1)
  SS BOND              : angle       1.20594 /  0.75 (    2)
  hydrogen bonds       : bond        0.04530 /  3.14 (  186)
  hydrogen bonds       : angle       4.33818 /  3.17 (  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
  48 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.077 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7396 (mmmm) cc_final: 0.7029 (mtmt)
REVERT: P   52 VAL cc_start: 0.6867 (p) cc_final: 0.6596 (t)
  outliers start: 11
  outliers final: 10
  residues processed: 42
  average time/residue: 0.0764
  time to fit residues: 4.0522
Evaluate side-chains
  47 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   70 LEU
Chi-restraints excluded: chain O residue  113 LEU
Chi-restraints excluded: chain P residue   47 LEU
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   55 SER
Chi-restraints excluded: chain Q residue   87 CYS
Chi-restraints excluded: chain Q residue   94 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.208882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.186437 restraints weight = 8525.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.190315 restraints weight = 4570.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.192914 restraints weight = 2801.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.194625 restraints weight = 1907.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.195796 restraints weight = 1422.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5647
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4988  Z= 0.191
  Angle     :  0.627   9.076   7108  Z= 0.335
  Chirality :  0.041   0.263    860
  Planarity :  0.005   0.055    635
  Dihedral  : 20.561 137.121   1625
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 25.80 %
    Favored  : 70.14 %
  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: -0.23 (0.42), residues: 408
  helix:  2.98 (1.55), residues: 12
  sheet:  0.61 (0.41), residues: 172
  loop : -0.97 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  74 
 TYR   0.018   0.003   TYR Q  31 
 PHE   0.013   0.003   PHE P  31 
 TRP   0.014   0.003   TRP Q  90 
 HIS   0.003   0.001   HIS O 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.19 ( 4987)
  covalent geometry    : angle       0.62623 /  0.33 ( 7106)
  SS BOND              : bond        0.01232 /  0.82 (    1)
  SS BOND              : angle       2.21334 /  1.41 (    2)
  hydrogen bonds       : bond        0.05678 /  3.87 (  186)
  hydrogen bonds       : angle       4.64571 /  3.36 (  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
  57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.131 
Fit side-chains
  outliers start: 14
  outliers final: 14
  residues processed: 51
  average time/residue: 0.0700
  time to fit residues: 4.5667
Evaluate side-chains
  57 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  135 ILE
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 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   87 CYS
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:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0270
   chunk 42 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Q   6 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 = 0.4613 r_free = 0.4613 target = 0.209201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.187722 restraints weight = 8680.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.191403 restraints weight = 4775.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.193884 restraints weight = 2992.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.195557 restraints weight = 2068.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.196715 restraints weight = 1551.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5607
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4988  Z= 0.121
  Angle     :  0.537   7.453   7108  Z= 0.295
  Chirality :  0.039   0.265    860
  Planarity :  0.005   0.052    635
  Dihedral  : 20.530 136.903   1625
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.38 %
    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: -0.14 (0.42), residues: 408
  helix:  3.10 (1.54), residues: 12
  sheet:  0.54 (0.42), residues: 162
  loop : -0.72 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P  18 
 TYR   0.012   0.002   TYR P  82 
 PHE   0.009   0.001   PHE O  25 
 TRP   0.012   0.002   TRP Q  90 
 HIS   0.005   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 4987)
  covalent geometry    : angle       0.53669 /  0.30 ( 7106)
  SS BOND              : bond        0.00782 /  0.52 (    1)
  SS BOND              : angle       1.13766 /  0.70 (    2)
  hydrogen bonds       : bond        0.04914 /  3.46 (  186)
  hydrogen bonds       : angle       4.52982 /  3.26 (  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
  51 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.075 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7309 (mmmm) cc_final: 0.6801 (mtmt)
REVERT: P   52 VAL cc_start: 0.6932 (p) cc_final: 0.6723 (t)
  outliers start: 11
  outliers final: 11
  residues processed: 47
  average time/residue: 0.0602
  time to fit residues: 3.6134
Evaluate side-chains
  50 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
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 P residue   19 SER
Chi-restraints excluded: chain P residue   30 THR
Chi-restraints excluded: chain P residue   47 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 16 optimal weight:    0.0970
   chunk 3 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.4116

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P   5 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 = 0.4618 r_free = 0.4618 target = 0.209771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.188020 restraints weight = 8556.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.191761 restraints weight = 4694.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.194237 restraints weight = 2929.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.195927 restraints weight = 2020.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.197064 restraints weight = 1511.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5607
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4988  Z= 0.118
  Angle     :  0.543   7.492   7108  Z= 0.295
  Chirality :  0.038   0.269    860
  Planarity :  0.004   0.053    635
  Dihedral  : 20.476 137.275   1625
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 25.51 %
    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: -0.12 (0.43), residues: 408
  helix:  3.10 (1.53), residues: 12
  sheet:  0.48 (0.42), residues: 167
  loop : -0.67 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  74 
 TYR   0.013   0.002   TYR P  82 
 PHE   0.007   0.001   PHE Q  61 
 TRP   0.011   0.002   TRP Q  90 
 HIS   0.004   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 4987)
  covalent geometry    : angle       0.54326 /  0.30 ( 7106)
  SS BOND              : bond        0.00810 /  0.54 (    1)
  SS BOND              : angle       1.07652 /  0.67 (    2)
  hydrogen bonds       : bond        0.04856 /  3.39 (  186)
  hydrogen bonds       : angle       4.42991 /  3.22 (  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
  53 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.133 
Fit side-chains
REVERT: O   22 LYS cc_start: 0.7242 (mmmm) cc_final: 0.6715 (mtmt)
REVERT: P   52 VAL cc_start: 0.6898 (p) cc_final: 0.6695 (t)
  outliers start: 12
  outliers final: 12
  residues processed: 48
  average time/residue: 0.0917
  time to fit residues: 5.5388
Evaluate side-chains
  52 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0970
   chunk 23 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P   5 GLN
** P  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.206455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.184839 restraints weight = 8519.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.188402 restraints weight = 4659.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.190793 restraints weight = 2923.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.192430 restraints weight = 2030.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.193537 restraints weight = 1532.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5701
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4988  Z= 0.181
  Angle     :  0.631   9.200   7108  Z= 0.344
  Chirality :  0.041   0.260    860
  Planarity :  0.005   0.055    635
  Dihedral  : 20.607 137.712   1625
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 26.38 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.42), residues: 408
  helix:  2.85 (1.56), residues: 12
  sheet:  0.30 (0.41), residues: 164
  loop : -0.88 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG P  74 
 TYR   0.021   0.003   TYR P  62 
 PHE   0.013   0.002   PHE O  83 
 TRP   0.014   0.002   TRP Q  90 
 HIS   0.004   0.001   HIS O 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 ( 4987)
  covalent geometry    : angle       0.62968 /  0.34 ( 7106)
  SS BOND              : bond        0.01183 /  0.79 (    1)
  SS BOND              : angle       2.22308 /  1.42 (    2)
  hydrogen bonds       : bond        0.05900 /  4.07 (  186)
  hydrogen bonds       : angle       4.67873 /  3.36 (  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
  58 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.128 
Fit side-chains
REVERT: O   13 LYS cc_start: 0.7387 (mttt) cc_final: 0.7184 (mttt)
REVERT: O   22 LYS cc_start: 0.7278 (mmmm) cc_final: 0.6765 (mtmt)
  outliers start: 13
  outliers final: 13
  residues processed: 53
  average time/residue: 0.0552
  time to fit residues: 3.9468
Evaluate side-chains
  56 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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 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 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=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:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0060
   chunk 18 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0770
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.3754

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P   5 GLN
** P  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4611 r_free = 0.4611 target = 0.208732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.186893 restraints weight = 8527.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.190578 restraints weight = 4665.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.193066 restraints weight = 2913.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.194730 restraints weight = 2016.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.195688 restraints weight = 1507.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5652
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4988  Z= 0.118
  Angle     :  0.583  13.325   7108  Z= 0.313
  Chirality :  0.038   0.266    860
  Planarity :  0.005   0.054    635
  Dihedral  : 20.531 137.355   1625
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 25.80 %
    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: -0.33 (0.42), residues: 408
  helix:  2.89 (1.54), residues: 12
  sheet:  0.31 (0.41), residues: 164
  loop : -0.77 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG P  74 
 TYR   0.015   0.002   TYR P  82 
 PHE   0.007   0.001   PHE O 108 
 TRP   0.012   0.002   TRP Q  90 
 HIS   0.003   0.001   HIS O 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 ( 4987)
  covalent geometry    : angle       0.58318 /  0.31 ( 7106)
  SS BOND              : bond        0.00776 /  0.52 (    1)
  SS BOND              : angle       0.86311 /  0.51 (    2)
  hydrogen bonds       : bond        0.05034 /  3.53 (  186)
  hydrogen bonds       : angle       4.54987 /  3.28 (  423)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 873.90 seconds
wall clock time: 15 minutes 44.81 seconds (944.81 seconds total)