Starting phenix.real_space_refine
on Wed Jul  1 21:45:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xzq_72368/07_2026/9xzq_72368.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      71      5.49       5
     S       7      5.16       5
     C    1673      2.51       5
     N     540      2.21       5
     O     799      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3090
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1511
          Classifications: {'RNA': 71}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 14, 'rna3p': 56}
    Chain: "B"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1551
          Classifications: {'peptide': 188}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 180}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'AN6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.67, per 1000 atoms: 0.22
  Number of scatterers: 3090
  At special positions: 0
  Unit cell: (53.56, 66.744, 81.576, 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       7     16.00
     P      71     15.00
     O     799      8.00
     N     540      7.00
     C    1673      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 55.0 milliseconds
  

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  362

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 1 sheets defined
      47.6% alpha, 9.0% beta
      17 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'B' and resid 103 through 107
      removed outlier: 3.665A  pdb=" N   MET B 107 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 128
    Processing helix  chain 'B' and resid 142 through 152
      removed outlier: 3.937A  pdb=" N   GLN B 146 " --> pdb=" O   LYS B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 5.741A  pdb=" N   TYR B 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   GLU B 158 " --> pdb=" O   THR B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 179 through 181
      No H-bonds generated for 'chain 'B' and resid 179 through 181'
    Processing helix  chain 'B' and resid 216 through 226
    Processing helix  chain 'B' and resid 247 through 262
      removed outlier: 3.595A  pdb=" N   PHE B 259 " --> pdb=" O   MET B 255 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP B 260 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 272
    Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 165
      removed outlier: 6.589A  pdb=" N   ILE B 135 " --> pdb=" O   LYS B 164 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE B  97 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLU B  96 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   VAL B 205 " --> pdb=" O   GLU B  96 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ILE B  98 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   VAL B 184 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 9.052A  pdb=" N   GLY B 206 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 9.040A  pdb=" N   LEU B 186 " --> pdb=" O   GLY B 206 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ARG B 230 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TYR B 185 " --> pdb=" O   ARG B 230 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    52 hydrogen bonds defined for protein.
    135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      45 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 0.47

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.02 -     1.18: 1
        1.18 -     1.34: 720
        1.34 -     1.49: 1459
        1.49 -     1.65: 1104
        1.65 -     1.81: 14
  Bond restraints: 3298
  Sorted by residual:
  bond pdb=" O3'   C A  64 "
       pdb=" P     U A  65 "
    ideal  model  delta    sigma   weight residual
    1.607  1.022  0.585 1.50e-02 4.44e+03 1.52e+03
  bond pdb=" N3    G A   9 "
       pdb=" C4    G A   9 "
    ideal  model  delta    sigma   weight residual
    1.350  1.486 -0.136 7.00e-03 2.04e+04 3.80e+02
  bond pdb=" C2    G A   9 "
       pdb=" N3    G A   9 "
    ideal  model  delta    sigma   weight residual
    1.323  1.472 -0.149 8.00e-03 1.56e+04 3.48e+02
  bond pdb=" C4'   G A   9 "
       pdb=" C3'   G A   9 "
    ideal  model  delta    sigma   weight residual
    1.527  1.266  0.261 1.50e-02 4.44e+03 3.02e+02
  bond pdb=" C4'   G A   9 "
       pdb=" O4'   G A   9 "
    ideal  model  delta    sigma   weight residual
    1.454  1.688 -0.234 1.50e-02 4.44e+03 2.43e+02
  ... (remaining 3293 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.09: 4790
       10.09 -    20.19: 6
       20.19 -    30.28: 2
       30.28 -    40.37: 1
       40.37 -    50.46: 2
  Bond angle restraints: 4801
  Sorted by residual:
  angle pdb=" C3'   G A   9 "
        pdb=" O3'   G A   9 "
        pdb=" P     G A  10 "
      ideal   model   delta    sigma   weight residual
     120.20  146.93  -26.73 1.50e+00 4.44e-01 3.18e+02
  angle pdb=" C5    G A   9 "
        pdb=" C4    G A   9 "
        pdb=" N3    G A   9 "
      ideal   model   delta    sigma   weight residual
     128.60  119.82    8.78 5.00e-01 4.00e+00 3.08e+02
  angle pdb=" C5    G A   9 "
        pdb=" C6    G A   9 "
        pdb=" O6    G A   9 "
      ideal   model   delta    sigma   weight residual
     128.60  118.12   10.48 6.00e-01 2.78e+00 3.05e+02
  angle pdb=" OP1   G A   9 "
        pdb=" P     G A   9 "
        pdb=" O5'   G A   9 "
      ideal   model   delta    sigma   weight residual
     108.00  158.46  -50.46 3.00e+00 1.11e-01 2.83e+02
  angle pdb=" C5    G A   9 "
        pdb=" C6    G A   9 "
        pdb=" N1    G A   9 "
      ideal   model   delta    sigma   weight residual
     111.50  119.63   -8.13 5.00e-01 4.00e+00 2.64e+02
  ... (remaining 4796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 1897
       35.95 -    71.90: 179
       71.90 -   107.85: 26
      107.85 -   143.80: 0
      143.80 -   179.75: 2
  Dihedral angle restraints: 2104
    sinusoidal: 1548
      harmonic: 556
  Sorted by residual:
  dihedral pdb=" C5'   G A   9 "
           pdb=" C4'   G A   9 "
           pdb=" C3'   G A   9 "
           pdb=" O3'   G A   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   83.79   63.21     1      8.00e+00 1.56e-02 8.24e+01
  dihedral pdb=" O4'   G A   9 "
           pdb=" C4'   G A   9 "
           pdb=" C3'   G A   9 "
           pdb=" C2'   G A   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -36.68   60.68     1      8.00e+00 1.56e-02 7.65e+01
  dihedral pdb=" C4'   G A   9 "
           pdb=" C3'   G A   9 "
           pdb=" C2'   G A   9 "
           pdb=" C1'   G A   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   21.16  -56.16     1      8.00e+00 1.56e-02 6.65e+01
  ... (remaining 2101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.480: 590
       0.480 -    0.959: 0
       0.959 -    1.439: 0
       1.439 -    1.919: 0
       1.919 -    2.398: 1
  Chirality restraints: 591
  Sorted by residual:
  chirality pdb=" P     G A   9 "
            pdb=" OP1   G A   9 "
            pdb=" OP2   G A   9 "
            pdb=" O5'   G A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.01    2.40 2.00e-01 2.50e+01 1.44e+02
  chirality pdb=" C3' AN6 A 101 "
            pdb=" C2' AN6 A 101 "
            pdb=" C4' AN6 A 101 "
            pdb=" O3' AN6 A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.39   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" C3'   G A   9 "
            pdb=" C4'   G A   9 "
            pdb=" O3'   G A   9 "
            pdb=" C2'   G A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.47   -0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 588 not shown)

  Planarity restraints: 349
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A  28 "   -0.029 2.00e-02 2.50e+03   2.30e-02 1.46e+01
        pdb=" N9    A A  28 "    0.057 2.00e-02 2.50e+03
        pdb=" C8    A A  28 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    A A  28 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    A A  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A A  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A A  28 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A A  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A A  28 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    A A  28 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    A A  28 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A  27 "   -0.034 2.00e-02 2.50e+03   1.99e-02 1.09e+01
        pdb=" N9    A A  27 "    0.054 2.00e-02 2.50e+03
        pdb=" C8    A A  27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A A  27 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A A  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A A  27 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A A  27 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A A  27 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A A  27 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A A  27 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A A  27 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  66 "    0.023 2.00e-02 2.50e+03   2.06e-02 9.55e+00
        pdb=" N1    U A  66 "   -0.050 2.00e-02 2.50e+03
        pdb=" C2    U A  66 "    0.027 2.00e-02 2.50e+03
        pdb=" O2    U A  66 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    U A  66 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U A  66 "    0.001 2.00e-02 2.50e+03
        pdb=" O4    U A  66 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    U A  66 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    U A  66 "    0.003 2.00e-02 2.50e+03
  ... (remaining 346 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 664
        2.78 -     3.31: 2896
        3.31 -     3.84: 5702
        3.84 -     4.37: 6603
        4.37 -     4.90: 9373
  Nonbonded interactions: 25238
  Sorted by model distance:
  nonbonded pdb=" C5    U A  24 "
            pdb=" N2    G A  44 "
     model   vdw
     2.249 3.420
  nonbonded pdb=" O2' AN6 A 101 "
            pdb=" O3' AN6 A 101 "
     model   vdw
     2.335 2.432
  nonbonded pdb=" O2'   A A  23 "
            pdb=" O5'   U A  24 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" O2'   G A   9 "
            pdb=" OG  SER B 114 "
     model   vdw
     2.411 3.040
  nonbonded pdb=" C3'   C A  64 "
            pdb=" OP2   U A  65 "
     model   vdw
     2.448 2.776
  ... (remaining 25233 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:             1.410
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.900
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
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      :  0.016   0.585   3299  Z= 1.130
  Angle     :  1.564  50.463   4801  Z= 0.943
  Chirality :  0.108   2.398    591
  Planarity :  0.004   0.026    349
  Dihedral  : 23.177 179.754   1742
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.61 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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 (0.69), residues: 186
  helix:  1.76 (0.70), residues: 64
  sheet:  0.08 (1.24), residues: 23
  loop : -0.41 (0.72), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 147 
 TYR   0.007   0.001   TYR B 237 
 PHE   0.004   0.001   PHE B 132 
 TRP   0.004   0.001   TRP B 160 
 HIS   0.001   0.001   HIS B 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01591 /  1.13 ( 3298)
  covalent geometry    : angle       1.56353 /  0.94 ( 4801)
  hydrogen bonds       : bond        0.14973 / 16.36 (   97)
  hydrogen bonds       : angle       9.03518 /  8.83 (  221)
  Misc. bond           : bond        0.01897 /  0.95 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.045 
Fit side-chains
   revert: symmetry clash
REVERT: B   98 ILE cc_start: 0.9020 (mm) cc_final: 0.8323 (mm)
REVERT: B  115 LEU cc_start: 0.9823 (tp) cc_final: 0.9589 (tt)
REVERT: B  124 SER cc_start: 0.9167 (p) cc_final: 0.8813 (t)
REVERT: B  140 PHE cc_start: 0.7493 (m-80) cc_final: 0.6910 (m-80)
REVERT: B  191 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8674 (mm-30)
REVERT: B  213 ARG cc_start: 0.9551 (ttm170) cc_final: 0.9141 (ttp-110)
REVERT: B  225 MET cc_start: 0.8579 (mmm) cc_final: 0.7745 (mmm)
REVERT: B  253 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: B  254 LEU cc_start: 0.9491 (mt) cc_final: 0.9255 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0624
  time to fit residues: 2.7083
Evaluate side-chains
  25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.079863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.066444 restraints weight = 21880.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.068331 restraints weight = 12356.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.069284 restraints weight = 8883.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.070176 restraints weight = 7383.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.070634 restraints weight = 6368.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3299  Z= 0.173
  Angle     :  0.616   7.431   4801  Z= 0.365
  Chirality :  0.039   0.325    591
  Planarity :  0.005   0.035    349
  Dihedral  : 23.755 179.412   1337
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.65 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.24 (0.64), residues: 186
  helix:  1.17 (0.62), residues: 64
  sheet: -0.67 (1.17), residues: 25
  loop : -0.21 (0.69), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 147 
 TYR   0.017   0.002   TYR B 185 
 PHE   0.011   0.002   PHE B 103 
 TRP   0.004   0.001   TRP B 264 
 HIS   0.012   0.002   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.17 ( 3298)
  covalent geometry    : angle       0.61554 /  0.37 ( 4801)
  hydrogen bonds       : bond        0.06064 /  6.10 (   97)
  hydrogen bonds       : angle       6.68823 /  6.57 (  221)
  Misc. bond           : bond        0.00808 /  0.40 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  109 ASP cc_start: 0.9042 (m-30) cc_final: 0.8763 (p0)
REVERT: B  124 SER cc_start: 0.9315 (p) cc_final: 0.8956 (t)
REVERT: B  140 PHE cc_start: 0.7486 (m-80) cc_final: 0.6996 (m-10)
REVERT: B  191 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: B  201 MET cc_start: 0.8035 (mmm) cc_final: 0.7789 (mmm)
REVERT: B  213 ARG cc_start: 0.9543 (ttm170) cc_final: 0.9184 (ttp-110)
REVERT: B  225 MET cc_start: 0.8254 (mmm) cc_final: 0.7966 (mmm)
REVERT: B  253 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8000 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 32
  average time/residue: 0.0395
  time to fit residues: 1.5646
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  218 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0870
   chunk 9 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.7162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.081045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.067568 restraints weight = 21332.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.069581 restraints weight = 11640.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.070813 restraints weight = 8208.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.071414 restraints weight = 6586.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.071894 restraints weight = 5829.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3299  Z= 0.130
  Angle     :  0.580   7.226   4801  Z= 0.335
  Chirality :  0.036   0.229    591
  Planarity :  0.005   0.032    349
  Dihedral  : 23.544 177.506   1337
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.12 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.04 (0.64), residues: 186
  helix:  1.21 (0.62), residues: 63
  sheet: -1.30 (1.12), residues: 28
  loop : -0.27 (0.68), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 143 
 TYR   0.005   0.001   TYR B 237 
 PHE   0.006   0.001   PHE B 140 
 TRP   0.004   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.13 ( 3298)
  covalent geometry    : angle       0.58048 /  0.34 ( 4801)
  hydrogen bonds       : bond        0.05867 /  5.43 (   97)
  hydrogen bonds       : angle       6.15783 /  6.21 (  221)
  Misc. bond           : bond        0.00080 /  0.04 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 ASP cc_start: 0.9004 (m-30) cc_final: 0.8704 (p0)
REVERT: B  124 SER cc_start: 0.9313 (p) cc_final: 0.8971 (t)
REVERT: B  140 PHE cc_start: 0.7623 (m-80) cc_final: 0.7019 (m-80)
REVERT: B  191 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8584 (mm-30)
REVERT: B  213 ARG cc_start: 0.9540 (ttm170) cc_final: 0.9161 (ttp-110)
REVERT: B  225 MET cc_start: 0.8351 (mmm) cc_final: 0.7998 (mmm)
REVERT: B  253 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8043 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0402
  time to fit residues: 1.5164
Evaluate side-chains
  24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  218 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 15 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0770
   overall best weight:    0.4340

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 146 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 = 0.3797 r_free = 0.3797 target = 0.080657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.067471 restraints weight = 21138.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.069460 restraints weight = 11817.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.070553 restraints weight = 8367.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.071411 restraints weight = 6843.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.071900 restraints weight = 5914.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3299  Z= 0.115
  Angle     :  0.513   6.520   4801  Z= 0.298
  Chirality :  0.034   0.152    591
  Planarity :  0.004   0.029    349
  Dihedral  : 23.356 177.357   1337
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.39 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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: -0.01 (0.63), residues: 186
  helix:  0.88 (0.62), residues: 64
  sheet: -1.21 (1.10), residues: 28
  loop : -0.11 (0.67), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 143 
 TYR   0.005   0.001   TYR B 237 
 PHE   0.006   0.001   PHE B 140 
 TRP   0.003   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.12 ( 3298)
  covalent geometry    : angle       0.51270 /  0.30 ( 4801)
  hydrogen bonds       : bond        0.05955 /  5.03 (   97)
  hydrogen bonds       : angle       5.86230 /  5.97 (  221)
  Misc. bond           : bond        0.00081 /  0.04 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 SER cc_start: 0.9316 (p) cc_final: 0.8973 (t)
REVERT: B  140 PHE cc_start: 0.7661 (m-80) cc_final: 0.7029 (m-10)
REVERT: B  191 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: B  201 MET cc_start: 0.7752 (mmm) cc_final: 0.7324 (mmm)
REVERT: B  213 ARG cc_start: 0.9551 (ttm170) cc_final: 0.9195 (ttp-110)
REVERT: B  225 MET cc_start: 0.8456 (mmm) cc_final: 0.8134 (mmm)
REVERT: B  253 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8032 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0561
  time to fit residues: 1.8598
Evaluate side-chains
  23 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  218 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 1 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 146 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 = 0.3699 r_free = 0.3699 target = 0.070608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.054198 restraints weight = 18919.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.056130 restraints weight = 10933.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.057245 restraints weight = 7973.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.058089 restraints weight = 6652.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.058463 restraints weight = 5856.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3299  Z= 0.140
  Angle     :  0.499   6.897   4801  Z= 0.288
  Chirality :  0.034   0.146    591
  Planarity :  0.005   0.053    349
  Dihedral  : 23.415 179.741   1337
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.23 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.20 (0.64), residues: 186
  helix:  0.92 (0.63), residues: 63
  sheet: -0.88 (1.02), residues: 33
  loop :  0.12 (0.70), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.008   0.001   TYR B 203 
 PHE   0.008   0.001   PHE B 259 
 TRP   0.003   0.001   TRP B 264 
 HIS   0.005   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.14 ( 3298)
  covalent geometry    : angle       0.49904 /  0.29 ( 4801)
  hydrogen bonds       : bond        0.06335 /  5.52 (   97)
  hydrogen bonds       : angle       5.72431 /  6.13 (  221)
  Misc. bond           : bond        0.00128 /  0.06 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.055 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7806 (mmm) cc_final: 0.7401 (mmm)
REVERT: B  109 ASP cc_start: 0.9076 (m-30) cc_final: 0.8804 (p0)
REVERT: B  124 SER cc_start: 0.9317 (p) cc_final: 0.8953 (t)
REVERT: B  140 PHE cc_start: 0.7534 (m-80) cc_final: 0.6990 (m-10)
REVERT: B  191 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8728 (mm-30)
REVERT: B  201 MET cc_start: 0.7871 (mmm) cc_final: 0.7418 (mmm)
REVERT: B  213 ARG cc_start: 0.9551 (ttm170) cc_final: 0.9202 (ttp-110)
REVERT: B  225 MET cc_start: 0.8497 (mmm) cc_final: 0.8163 (mmm)
REVERT: B  253 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8215 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0805
  time to fit residues: 2.6885
Evaluate side-chains
  24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  218 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3737 r_free = 0.3737 target = 0.076471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.062931 restraints weight = 21795.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.064861 restraints weight = 11960.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.065913 restraints weight = 8444.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.066689 restraints weight = 6944.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.067103 restraints weight = 6048.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3299  Z= 0.142
  Angle     :  0.549   9.117   4801  Z= 0.319
  Chirality :  0.034   0.160    591
  Planarity :  0.004   0.029    349
  Dihedral  : 23.473 179.810   1337
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.97 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.19 (0.63), residues: 186
  helix:  0.74 (0.62), residues: 63
  sheet: -0.82 (1.03), residues: 33
  loop :  0.24 (0.69), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.007   0.001   TYR B 123 
 PHE   0.009   0.001   PHE B 259 
 TRP   0.003   0.001   TRP B 264 
 HIS   0.002   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 3298)
  covalent geometry    : angle       0.54886 /  0.32 ( 4801)
  hydrogen bonds       : bond        0.06576 /  5.56 (   97)
  hydrogen bonds       : angle       5.76240 /  6.15 (  221)
  Misc. bond           : bond        0.00040 /  0.02 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.047 
Fit side-chains
REVERT: B  109 ASP cc_start: 0.9023 (m-30) cc_final: 0.8718 (p0)
REVERT: B  124 SER cc_start: 0.9323 (p) cc_final: 0.8945 (t)
REVERT: B  140 PHE cc_start: 0.7592 (m-80) cc_final: 0.7033 (m-10)
REVERT: B  191 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: B  201 MET cc_start: 0.8044 (mmm) cc_final: 0.7691 (mmm)
REVERT: B  213 ARG cc_start: 0.9533 (ttm170) cc_final: 0.9183 (ttp-110)
REVERT: B  225 MET cc_start: 0.8407 (mmm) cc_final: 0.8053 (mmm)
REVERT: B  253 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7969 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0535
  time to fit residues: 1.7902
Evaluate side-chains
  25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0000
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.077160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.063749 restraints weight = 21714.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.065706 restraints weight = 11648.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.066807 restraints weight = 8133.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.067622 restraints weight = 6598.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.067895 restraints weight = 5693.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3299  Z= 0.104
  Angle     :  0.502   7.091   4801  Z= 0.298
  Chirality :  0.034   0.169    591
  Planarity :  0.004   0.025    349
  Dihedral  : 23.509 179.511   1337
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.54 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.18 (0.64), residues: 186
  helix:  0.59 (0.62), residues: 63
  sheet: -0.91 (1.02), residues: 34
  loop :  0.41 (0.70), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 143 
 TYR   0.005   0.001   TYR B 237 
 PHE   0.005   0.001   PHE B 259 
 TRP   0.002   0.001   TRP B 264 
 HIS   0.001   0.000   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.10 ( 3298)
  covalent geometry    : angle       0.50177 /  0.30 ( 4801)
  hydrogen bonds       : bond        0.05954 /  4.79 (   97)
  hydrogen bonds       : angle       5.66255 /  6.09 (  221)
  Misc. bond           : bond        0.00050 /  0.02 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.048 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7655 (mmm) cc_final: 0.7364 (mmm)
REVERT: B  109 ASP cc_start: 0.9013 (m-30) cc_final: 0.8733 (p0)
REVERT: B  124 SER cc_start: 0.9282 (p) cc_final: 0.8912 (t)
REVERT: B  140 PHE cc_start: 0.7670 (m-80) cc_final: 0.7060 (m-10)
REVERT: B  191 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8642 (mm-30)
REVERT: B  201 MET cc_start: 0.8058 (mmm) cc_final: 0.7654 (mmm)
REVERT: B  213 ARG cc_start: 0.9537 (ttm170) cc_final: 0.9187 (ttp-110)
REVERT: B  225 MET cc_start: 0.8402 (mmm) cc_final: 0.8038 (mmm)
REVERT: B  253 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8042 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 28
  average time/residue: 0.0635
  time to fit residues: 2.1586
Evaluate side-chains
  28 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  246 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    0.0770
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   overall best weight:    2.0942

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 262 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.073479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.060135 restraints weight = 22178.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.061899 restraints weight = 12223.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.062883 restraints weight = 8794.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.063595 restraints weight = 7308.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.063862 restraints weight = 6471.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3299  Z= 0.165
  Angle     :  0.568   7.246   4801  Z= 0.332
  Chirality :  0.036   0.182    591
  Planarity :  0.005   0.026    349
  Dihedral  : 23.643 177.858   1337
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.97 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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: -0.22 (0.64), residues: 186
  helix: -0.00 (0.62), residues: 62
  sheet: -0.76 (1.03), residues: 34
  loop :  0.22 (0.71), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 147 
 TYR   0.008   0.002   TYR B 123 
 PHE   0.012   0.002   PHE B 259 
 TRP   0.003   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 ( 3298)
  covalent geometry    : angle       0.56821 /  0.33 ( 4801)
  hydrogen bonds       : bond        0.07752 /  6.84 (   97)
  hydrogen bonds       : angle       5.81188 /  6.05 (  221)
  Misc. bond           : bond        0.00014 /  0.01 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.079 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7601 (mmm) cc_final: 0.7340 (mmm)
REVERT: B  109 ASP cc_start: 0.9101 (m-30) cc_final: 0.8833 (p0)
REVERT: B  124 SER cc_start: 0.9309 (p) cc_final: 0.8932 (t)
REVERT: B  140 PHE cc_start: 0.8051 (m-80) cc_final: 0.7434 (m-10)
REVERT: B  191 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8798 (mm-30)
REVERT: B  201 MET cc_start: 0.7874 (mmm) cc_final: 0.7446 (mmm)
REVERT: B  213 ARG cc_start: 0.9507 (ttm170) cc_final: 0.9156 (ttp-110)
REVERT: B  225 MET cc_start: 0.8408 (mmm) cc_final: 0.8053 (mmm)
REVERT: B  253 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: B  254 LEU cc_start: 0.9676 (mt) cc_final: 0.9431 (mt)
  outliers start: 6
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0702
  time to fit residues: 2.2891
Evaluate side-chains
  28 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0870
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6360

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.067452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.051018 restraints weight = 19082.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.052937 restraints weight = 10543.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.054156 restraints weight = 7561.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.054902 restraints weight = 6171.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.055240 restraints weight = 5441.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3299  Z= 0.109
  Angle     :  0.540   9.337   4801  Z= 0.320
  Chirality :  0.034   0.160    591
  Planarity :  0.004   0.025    349
  Dihedral  : 23.608 179.177   1337
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 24.86 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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: -0.04 (0.64), residues: 186
  helix:  0.15 (0.62), residues: 62
  sheet: -0.73 (1.01), residues: 34
  loop :  0.36 (0.72), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 147 
 TYR   0.006   0.001   TYR B 237 
 PHE   0.007   0.001   PHE B 259 
 TRP   0.006   0.001   TRP B 160 
 HIS   0.001   0.000   HIS B 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.11 ( 3298)
  covalent geometry    : angle       0.53981 /  0.32 ( 4801)
  hydrogen bonds       : bond        0.06102 /  5.16 (   97)
  hydrogen bonds       : angle       5.83052 /  6.02 (  221)
  Misc. bond           : bond        0.00027 /  0.01 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 MET cc_start: 0.7658 (mmm) cc_final: 0.7364 (mmm)
REVERT: B  109 ASP cc_start: 0.9062 (m-30) cc_final: 0.8800 (p0)
REVERT: B  124 SER cc_start: 0.9272 (p) cc_final: 0.8899 (t)
REVERT: B  140 PHE cc_start: 0.7726 (m-80) cc_final: 0.7171 (m-10)
REVERT: B  191 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8702 (mm-30)
REVERT: B  201 MET cc_start: 0.8284 (mmm) cc_final: 0.7892 (mmm)
REVERT: B  213 ARG cc_start: 0.9518 (ttm170) cc_final: 0.9176 (ttp-110)
REVERT: B  225 MET cc_start: 0.8405 (mmm) cc_final: 0.8038 (mmm)
REVERT: B  253 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: B  254 LEU cc_start: 0.9689 (mt) cc_final: 0.9339 (mt)
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0849
  time to fit residues: 2.6683
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0870
   chunk 5 optimal weight:   10.9990
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9962

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.074162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.061119 restraints weight = 21651.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.062941 restraints weight = 11467.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.064068 restraints weight = 8033.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.064657 restraints weight = 6478.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.065164 restraints weight = 5754.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3299  Z= 0.118
  Angle     :  0.529   9.724   4801  Z= 0.312
  Chirality :  0.034   0.165    591
  Planarity :  0.004   0.024    349
  Dihedral  : 23.577 179.965   1337
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.28 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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:  0.00 (0.65), residues: 186
  helix:  0.18 (0.63), residues: 61
  sheet: -0.55 (1.01), residues: 34
  loop :  0.31 (0.72), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.005   0.001   TYR B 258 
 PHE   0.008   0.001   PHE B 259 
 TRP   0.002   0.000   TRP B 160 
 HIS   0.002   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.12 ( 3298)
  covalent geometry    : angle       0.52941 /  0.31 ( 4801)
  hydrogen bonds       : bond        0.05972 /  4.88 (   97)
  hydrogen bonds       : angle       5.76536 /  5.96 (  221)
  Misc. bond           : bond        0.00013 /  0.01 (    1)

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

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

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  372 Ramachandran restraints generated.
    186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 MET cc_start: 0.7705 (mmm) cc_final: 0.7428 (mmm)
REVERT: B  109 ASP cc_start: 0.9084 (m-30) cc_final: 0.8848 (p0)
REVERT: B  124 SER cc_start: 0.9247 (p) cc_final: 0.8888 (t)
REVERT: B  140 PHE cc_start: 0.7948 (m-80) cc_final: 0.7352 (m-10)
REVERT: B  191 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8707 (mm-30)
REVERT: B  201 MET cc_start: 0.8139 (mmm) cc_final: 0.7764 (mmm)
REVERT: B  213 ARG cc_start: 0.9519 (ttm170) cc_final: 0.9171 (ttp-110)
REVERT: B  225 MET cc_start: 0.8369 (mmm) cc_final: 0.8009 (mmm)
REVERT: B  253 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8345 (tm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0926
  time to fit residues: 2.9096
Evaluate side-chains
  27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  268 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8540

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.074288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.061001 restraints weight = 22170.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.062947 restraints weight = 11874.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.064078 restraints weight = 8273.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.064794 restraints weight = 6657.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.065173 restraints weight = 5804.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   3299  Z= 0.110
  Angle     :  0.541  10.461   4801  Z= 0.319
  Chirality :  0.035   0.213    591
  Planarity :  0.004   0.023    349
  Dihedral  : 23.538 179.851   1337
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.28 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 28.57 %
    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: -0.02 (0.65), residues: 186
  helix:  0.08 (0.63), residues: 61
  sheet: -0.55 (1.00), residues: 34
  loop :  0.36 (0.73), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 147 
 TYR   0.005   0.001   TYR B 258 
 PHE   0.005   0.001   PHE B 259 
 TRP   0.005   0.001   TRP B 160 
 HIS   0.003   0.001   HIS B 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.11 ( 3298)
  covalent geometry    : angle       0.54146 /  0.32 ( 4801)
  hydrogen bonds       : bond        0.05973 /  4.84 (   97)
  hydrogen bonds       : angle       5.81974 /  5.90 (  221)
  Misc. bond           : bond        0.00022 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 769.17 seconds
wall clock time: 13 minutes 57.72 seconds (837.72 seconds total)