Starting phenix.real_space_refine
on Tue Feb  3 13:21:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xzq_72368/02_2026/9xzq_72368_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xzq_72368/02_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_72368/02_2026/9xzq_72368_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xzq_72368/02_2026/9xzq_72368_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xzq_72368/02_2026/9xzq_72368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xzq_72368/02_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-2.0-5952/lib/python3.9/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: 1.04, per 1000 atoms: 0.34
  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: 0.34
  Conformation dependent library (CDL) restraints added in 64.9 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: 0.29
  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: 0.42

  Time building geometry restraints manager: 0.39 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=" 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
  bond pdb=" C2' AN6 A 101 "
       pdb=" C3' AN6 A 101 "
    ideal  model  delta    sigma   weight residual
    1.532  1.289  0.243 2.00e-02 2.50e+03 1.47e+02
  bond pdb=" C6  AN6 A 101 "
       pdb=" N6  AN6 A 101 "
    ideal  model  delta    sigma   weight residual
    1.334  1.519 -0.185 2.00e-02 2.50e+03 8.59e+01
  ... (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=" 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=" O3'   U A   8 "
        pdb=" P     G A   9 "
        pdb=" OP2   G A   9 "
      ideal   model   delta    sigma   weight residual
     108.00  155.92  -47.92 3.00e+00 1.11e-01 2.55e+02
  angle pdb=" OP1   G A   9 "
        pdb=" P     G A   9 "
        pdb=" OP2   G A   9 "
      ideal   model   delta    sigma   weight residual
     119.60   79.25   40.35 3.00e+00 1.11e-01 1.81e+02
  angle pdb=" O3'   U A   8 "
        pdb=" P     G A   9 "
        pdb=" O5'   G A   9 "
      ideal   model   delta    sigma   weight residual
     104.00   89.30   14.70 1.50e+00 4.44e-01 9.61e+01
  ... (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:             1.040
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.880
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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= 0.970
  Angle     :  1.563  50.463   4801  Z= 0.684
  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
  covalent geometry    : bond        0.01591 ( 3298)
  covalent geometry    : angle       1.56348 ( 4801)
  hydrogen bonds       : bond        0.14973 (   97)
  hydrogen bonds       : angle       9.03518 (  221)
  Misc. bond           : bond        0.01897 (    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  : 0.050 
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: 0.0687
  time to fit residues: 2.9172
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  : 0.049 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 212 ASN
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.079856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.066415 restraints weight = 21862.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.068340 restraints weight = 12254.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.069571 restraints weight = 8720.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.070139 restraints weight = 7034.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.070677 restraints weight = 6279.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3299  Z= 0.160
  Angle     :  0.667   9.754   4801  Z= 0.338
  Chirality :  0.036   0.308    591
  Planarity :  0.005   0.034    349
  Dihedral  : 23.587 175.813   1337
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.50 %
    Favored  : 79.77 %
  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:  0.58 (0.67), residues: 186
  helix:  1.65 (0.64), residues: 64
  sheet: -0.89 (1.13), residues: 28
  loop :  0.01 (0.72), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 143 
 TYR   0.013   0.002   TYR B 185 
 PHE   0.010   0.001   PHE B 259 
 TRP   0.004   0.001   TRP B 264 
 HIS   0.002   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3298)
  covalent geometry    : angle       0.66658 ( 4801)
  hydrogen bonds       : bond        0.05687 (   97)
  hydrogen bonds       : angle       5.98806 (  221)
  Misc. bond           : bond        0.00037 (    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
  33 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  109 ASP cc_start: 0.9053 (m-30) cc_final: 0.8773 (p0)
REVERT: B  124 SER cc_start: 0.9301 (p) cc_final: 0.8923 (t)
REVERT: B  140 PHE cc_start: 0.7485 (m-80) cc_final: 0.6937 (m-80)
REVERT: B  191 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8607 (mm-30)
REVERT: B  213 ARG cc_start: 0.9549 (ttm170) cc_final: 0.9163 (ttp-110)
REVERT: B  225 MET cc_start: 0.8373 (mmm) cc_final: 0.8024 (mmm)
REVERT: B  250 HIS cc_start: 0.9360 (m90) cc_final: 0.9148 (m90)
REVERT: B  253 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: B  254 LEU cc_start: 0.9525 (mt) cc_final: 0.9272 (mt)
  outliers start: 3
  outliers final: 1
  residues processed: 31
  average time/residue: 0.0662
  time to fit residues: 2.5616
Evaluate side-chains
  25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.072547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.056365 restraints weight = 18524.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.058431 restraints weight = 10572.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.059588 restraints weight = 7625.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.060468 restraints weight = 6299.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.060979 restraints weight = 5532.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3299  Z= 0.122
  Angle     :  0.562   7.829   4801  Z= 0.277
  Chirality :  0.031   0.134    591
  Planarity :  0.004   0.029    349
  Dihedral  : 23.311 178.200   1337
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 20.23 %
    Favored  : 78.03 %
  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:  0.66 (0.67), residues: 186
  helix:  1.87 (0.69), residues: 64
  sheet: -0.80 (1.04), residues: 33
  loop : -0.03 (0.72), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 143 
 TYR   0.005   0.001   TYR B 237 
 PHE   0.007   0.001   PHE B 259 
 TRP   0.006   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3298)
  covalent geometry    : angle       0.56154 ( 4801)
  hydrogen bonds       : bond        0.05056 (   97)
  hydrogen bonds       : angle       5.53473 (  221)
  Misc. bond           : bond        0.00104 (    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
  29 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B  109 ASP cc_start: 0.9064 (m-30) cc_final: 0.8717 (p0)
REVERT: B  124 SER cc_start: 0.9293 (p) cc_final: 0.8918 (t)
REVERT: B  140 PHE cc_start: 0.7542 (m-80) cc_final: 0.6969 (m-10)
REVERT: B  191 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8667 (mm-30)
REVERT: B  213 ARG cc_start: 0.9570 (ttm170) cc_final: 0.9211 (ttp-110)
REVERT: B  225 MET cc_start: 0.8495 (mmm) cc_final: 0.8148 (mmm)
REVERT: B  250 HIS cc_start: 0.9374 (m90) cc_final: 0.9159 (m90)
REVERT: B  253 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: B  254 LEU cc_start: 0.9560 (mt) cc_final: 0.9313 (mt)
  outliers start: 3
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0810
  time to fit residues: 2.6570
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  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  184 VAL
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:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 117 ASN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 ASN
B 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.072819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.059170 restraints weight = 21286.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.061059 restraints weight = 11962.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.061953 restraints weight = 8645.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.062658 restraints weight = 7263.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.063013 restraints weight = 6440.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3299  Z= 0.180
  Angle     :  0.649   8.317   4801  Z= 0.323
  Chirality :  0.034   0.129    591
  Planarity :  0.005   0.037    349
  Dihedral  : 23.681 177.679   1337
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 19.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.65 %
    Favored  : 78.03 %
  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:  0.57 (0.67), residues: 186
  helix:  1.62 (0.68), residues: 64
  sheet: -0.74 (1.04), residues: 34
  loop :  0.03 (0.72), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 202 
 TYR   0.012   0.002   TYR B 123 
 PHE   0.012   0.002   PHE B 259 
 TRP   0.004   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3298)
  covalent geometry    : angle       0.64884 ( 4801)
  hydrogen bonds       : bond        0.06874 (   97)
  hydrogen bonds       : angle       5.48205 (  221)
  Misc. bond           : bond        0.00058 (    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  : 0.052 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7563 (mmt) cc_final: 0.7273 (mmm)
REVERT: B  109 ASP cc_start: 0.9143 (m-30) cc_final: 0.8741 (p0)
REVERT: B  124 SER cc_start: 0.9357 (p) cc_final: 0.8977 (t)
REVERT: B  140 PHE cc_start: 0.7910 (m-80) cc_final: 0.7318 (m-80)
REVERT: B  213 ARG cc_start: 0.9509 (ttm170) cc_final: 0.9117 (ttp-110)
REVERT: B  225 MET cc_start: 0.8501 (mmm) cc_final: 0.8120 (mmm)
REVERT: B  250 HIS cc_start: 0.9551 (m90) cc_final: 0.9328 (m90)
REVERT: B  253 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: B  254 LEU cc_start: 0.9637 (mt) cc_final: 0.9387 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0626
  time to fit residues: 2.0075
Evaluate side-chains
  26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 VAL
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:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0170
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.1420

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3674 r_free = 0.3674 target = 0.073530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.060119 restraints weight = 22245.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.062009 restraints weight = 12028.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.062976 restraints weight = 8532.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.063737 restraints weight = 7075.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.064138 restraints weight = 6199.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3299  Z= 0.121
  Angle     :  0.546   5.720   4801  Z= 0.272
  Chirality :  0.032   0.160    591
  Planarity :  0.004   0.026    349
  Dihedral  : 23.788 179.460   1337
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 21.39 %
    Favored  : 76.88 %
  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:  0.78 (0.66), residues: 186
  helix:  1.57 (0.65), residues: 64
  sheet: -0.72 (1.03), residues: 34
  loop :  0.40 (0.73), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 121 
 TYR   0.009   0.001   TYR B 258 
 PHE   0.008   0.001   PHE B 259 
 TRP   0.004   0.001   TRP B 160 
 HIS   0.002   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3298)
  covalent geometry    : angle       0.54560 ( 4801)
  hydrogen bonds       : bond        0.05139 (   97)
  hydrogen bonds       : angle       5.23761 (  221)
  Misc. bond           : bond        0.00011 (    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: 3
    poor density    : 27
  time to evaluate  : 0.048 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 MET cc_start: 0.7549 (mmt) cc_final: 0.7273 (mmm)
REVERT: B  109 ASP cc_start: 0.9171 (m-30) cc_final: 0.8846 (p0)
REVERT: B  124 SER cc_start: 0.9298 (p) cc_final: 0.8914 (t)
REVERT: B  140 PHE cc_start: 0.8002 (m-80) cc_final: 0.7341 (m-80)
REVERT: B  185 TYR cc_start: 0.7955 (t80) cc_final: 0.7668 (t80)
REVERT: B  201 MET cc_start: 0.8081 (mmm) cc_final: 0.7362 (tpp)
REVERT: B  213 ARG cc_start: 0.9504 (ttm170) cc_final: 0.9109 (ttp-110)
REVERT: B  221 LYS cc_start: 0.9293 (tttt) cc_final: 0.9030 (tptp)
REVERT: B  225 MET cc_start: 0.8481 (mmm) cc_final: 0.7754 (mmm)
REVERT: B  250 HIS cc_start: 0.9574 (m90) cc_final: 0.9333 (m90)
REVERT: B  253 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: B  254 LEU cc_start: 0.9674 (mt) cc_final: 0.9349 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0400
  time to fit residues: 1.4628
Evaluate side-chains
  26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  184 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.069061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.055893 restraints weight = 22820.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.057701 restraints weight = 11750.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.058650 restraints weight = 8286.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.059393 restraints weight = 6837.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.059563 restraints weight = 5974.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3299  Z= 0.182
  Angle     :  0.600   6.078   4801  Z= 0.303
  Chirality :  0.034   0.140    591
  Planarity :  0.005   0.030    349
  Dihedral  : 23.997 177.017   1337
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.23 %
    Favored  : 75.14 %
  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:  0.66 (0.67), residues: 186
  helix:  1.32 (0.66), residues: 64
  sheet: -0.50 (1.04), residues: 34
  loop :  0.33 (0.75), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 143 
 TYR   0.008   0.001   TYR B 237 
 PHE   0.016   0.002   PHE B 259 
 TRP   0.006   0.001   TRP B 160 
 HIS   0.005   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3298)
  covalent geometry    : angle       0.59994 ( 4801)
  hydrogen bonds       : bond        0.06627 (   97)
  hydrogen bonds       : angle       5.34036 (  221)
  Misc. bond           : bond        0.00047 (    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
  33 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.051 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7806 (mmt) cc_final: 0.7488 (mmm)
REVERT: B  109 ASP cc_start: 0.9272 (m-30) cc_final: 0.8888 (p0)
REVERT: B  124 SER cc_start: 0.9330 (p) cc_final: 0.8919 (t)
REVERT: B  140 PHE cc_start: 0.7959 (m-80) cc_final: 0.7420 (m-80)
REVERT: B  185 TYR cc_start: 0.7928 (t80) cc_final: 0.7619 (t80)
REVERT: B  201 MET cc_start: 0.8197 (mmm) cc_final: 0.7583 (tpp)
REVERT: B  213 ARG cc_start: 0.9445 (ttm170) cc_final: 0.9052 (ttp-110)
REVERT: B  221 LYS cc_start: 0.9338 (tttt) cc_final: 0.9084 (tptp)
REVERT: B  225 MET cc_start: 0.8462 (mmm) cc_final: 0.7773 (mmm)
REVERT: B  253 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: B  254 LEU cc_start: 0.9716 (mt) cc_final: 0.9458 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0558
  time to fit residues: 1.9612
Evaluate side-chains
  32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  251 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.066394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.053365 restraints weight = 23375.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.055113 restraints weight = 12052.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.056166 restraints weight = 8436.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.056732 restraints weight = 6832.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.057145 restraints weight = 6075.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.6553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3299  Z= 0.212
  Angle     :  0.646   7.056   4801  Z= 0.334
  Chirality :  0.036   0.177    591
  Planarity :  0.005   0.045    349
  Dihedral  : 24.283 176.227   1337
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 20.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.70 %
    Favored  : 72.83 %
  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 (0.64), residues: 186
  helix:  0.35 (0.60), residues: 63
  sheet: -0.60 (1.01), residues: 34
  loop :  0.19 (0.74), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 213 
 TYR   0.008   0.002   TYR B 214 
 PHE   0.017   0.002   PHE B 259 
 TRP   0.008   0.002   TRP B 160 
 HIS   0.002   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3298)
  covalent geometry    : angle       0.64605 ( 4801)
  hydrogen bonds       : bond        0.07679 (   97)
  hydrogen bonds       : angle       5.46130 (  221)
  Misc. bond           : bond        0.00050 (    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
  33 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B  109 ASP cc_start: 0.9368 (m-30) cc_final: 0.8943 (p0)
REVERT: B  117 ASN cc_start: 0.9369 (m110) cc_final: 0.9143 (m110)
REVERT: B  140 PHE cc_start: 0.8114 (m-80) cc_final: 0.7571 (m-10)
REVERT: B  201 MET cc_start: 0.8152 (mmm) cc_final: 0.7616 (tpp)
REVERT: B  213 ARG cc_start: 0.9490 (ttm170) cc_final: 0.9083 (ttp-110)
REVERT: B  225 MET cc_start: 0.8729 (mmm) cc_final: 0.8391 (mmm)
REVERT: B  250 HIS cc_start: 0.9557 (m90) cc_final: 0.9129 (m90)
  outliers start: 6
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0959
  time to fit residues: 3.2654
Evaluate side-chains
  28 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  251 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    2.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.057745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.042846 restraints weight = 19044.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.044504 restraints weight = 9841.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.045586 restraints weight = 6839.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.046202 restraints weight = 5481.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.046700 restraints weight = 4818.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.7497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3299  Z= 0.223
  Angle     :  0.678   9.481   4801  Z= 0.356
  Chirality :  0.039   0.223    591
  Planarity :  0.005   0.034    349
  Dihedral  : 24.320 178.001   1337
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 23.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 23.12 %
    Favored  : 71.10 %
  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:  0.09 (0.66), residues: 186
  helix:  0.66 (0.63), residues: 61
  sheet: -0.72 (1.00), residues: 34
  loop :  0.12 (0.76), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 231 
 TYR   0.007   0.001   TYR B 185 
 PHE   0.016   0.002   PHE B 259 
 TRP   0.009   0.002   TRP B 160 
 HIS   0.003   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 3298)
  covalent geometry    : angle       0.67795 ( 4801)
  hydrogen bonds       : bond        0.07701 (   97)
  hydrogen bonds       : angle       5.68299 (  221)
  Misc. bond           : bond        0.00012 (    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
  37 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 ASP cc_start: 0.9447 (m-30) cc_final: 0.9052 (p0)
REVERT: B  117 ASN cc_start: 0.9447 (m110) cc_final: 0.9211 (m110)
REVERT: B  140 PHE cc_start: 0.8254 (m-80) cc_final: 0.7709 (m-10)
REVERT: B  201 MET cc_start: 0.8192 (mmm) cc_final: 0.7684 (tpp)
REVERT: B  213 ARG cc_start: 0.9434 (ttm170) cc_final: 0.9084 (ttp-110)
REVERT: B  225 MET cc_start: 0.8686 (mmm) cc_final: 0.8382 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 32
  average time/residue: 0.0936
  time to fit residues: 3.5010
Evaluate side-chains
  32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
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  148 PHE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  251 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.059215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.043453 restraints weight = 19609.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.045262 restraints weight = 9993.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.046456 restraints weight = 6892.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.047197 restraints weight = 5521.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.047638 restraints weight = 4812.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.7630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3299  Z= 0.134
  Angle     :  0.650  11.449   4801  Z= 0.332
  Chirality :  0.038   0.220    591
  Planarity :  0.004   0.030    349
  Dihedral  : 24.154 177.426   1337
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 26.01 %
    Favored  : 69.94 %
  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: -0.09 (0.67), residues: 186
  helix:  0.14 (0.63), residues: 62
  sheet: -0.81 (0.97), residues: 34
  loop :  0.32 (0.77), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 121 
 TYR   0.013   0.002   TYR B 185 
 PHE   0.006   0.001   PHE B 140 
 TRP   0.006   0.001   TRP B 160 
 HIS   0.004   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3298)
  covalent geometry    : angle       0.64987 ( 4801)
  hydrogen bonds       : bond        0.05908 (   97)
  hydrogen bonds       : angle       5.45619 (  221)
  Misc. bond           : bond        0.00018 (    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
  33 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.084 
Fit side-chains
REVERT: B  109 ASP cc_start: 0.9397 (m-30) cc_final: 0.8996 (p0)
REVERT: B  124 SER cc_start: 0.9226 (p) cc_final: 0.8783 (t)
REVERT: B  140 PHE cc_start: 0.8256 (m-80) cc_final: 0.7657 (m-10)
REVERT: B  201 MET cc_start: 0.8172 (mmm) cc_final: 0.7711 (tpp)
REVERT: B  213 ARG cc_start: 0.9483 (ttm170) cc_final: 0.9074 (ttp-110)
REVERT: B  225 MET cc_start: 0.8755 (mmm) cc_final: 0.8435 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0758
  time to fit residues: 2.6711
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  : 0.079 
-------------------------------------------------------------------------------
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  148 PHE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  251 VAL
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:    0.2980
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.067253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.054833 restraints weight = 22475.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.056726 restraints weight = 11610.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.057798 restraints weight = 8060.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.058350 restraints weight = 6482.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.058567 restraints weight = 5709.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.7772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3299  Z= 0.168
  Angle     :  0.670   9.259   4801  Z= 0.354
  Chirality :  0.038   0.222    591
  Planarity :  0.005   0.030    349
  Dihedral  : 24.155 177.662   1337
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.59 %
    Favored  : 69.94 %
  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: -0.16 (0.67), residues: 186
  helix: -0.04 (0.64), residues: 61
  sheet: -0.82 (0.97), residues: 34
  loop :  0.37 (0.77), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 147 
 TYR   0.006   0.001   TYR B 185 
 PHE   0.009   0.001   PHE B 259 
 TRP   0.006   0.001   TRP B 160 
 HIS   0.003   0.001   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3298)
  covalent geometry    : angle       0.67007 ( 4801)
  hydrogen bonds       : bond        0.06688 (   97)
  hydrogen bonds       : angle       5.85264 (  221)
  Misc. bond           : bond        0.00022 (    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: 6
    poor density    : 23
  time to evaluate  : 0.088 
Fit side-chains
REVERT: B  107 MET cc_start: 0.7191 (mmm) cc_final: 0.6957 (mmm)
REVERT: B  109 ASP cc_start: 0.9408 (m-30) cc_final: 0.9025 (p0)
REVERT: B  140 PHE cc_start: 0.8383 (m-80) cc_final: 0.7804 (m-10)
REVERT: B  201 MET cc_start: 0.8067 (mmm) cc_final: 0.7543 (tpp)
REVERT: B  213 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9087 (ttp-110)
REVERT: B  225 MET cc_start: 0.8734 (mmm) cc_final: 0.8420 (mmm)
  outliers start: 6
  outliers final: 6
  residues processed: 26
  average time/residue: 0.0770
  time to fit residues: 2.4352
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  : 0.086 
-------------------------------------------------------------------------------
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  148 PHE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  251 VAL
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:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.061350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046418 restraints weight = 19472.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.048289 restraints weight = 9778.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.049490 restraints weight = 6665.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.050173 restraints weight = 5313.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.050744 restraints weight = 4652.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.7986

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= 0.132
  Angle     :  0.654   9.409   4801  Z= 0.343
  Chirality :  0.037   0.214    591
  Planarity :  0.004   0.033    349
  Dihedral  : 23.985 172.194   1337
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.59 %
    Favored  : 69.94 %
  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: -0.05 (0.67), residues: 186
  helix: -0.12 (0.62), residues: 61
  sheet: -0.77 (0.97), residues: 34
  loop :  0.58 (0.78), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 121 
 TYR   0.008   0.001   TYR B 185 
 PHE   0.004   0.001   PHE B 132 
 TRP   0.003   0.001   TRP B 160 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3298)
  covalent geometry    : angle       0.65353 ( 4801)
  hydrogen bonds       : bond        0.05991 (   97)
  hydrogen bonds       : angle       5.74829 (  221)
  Misc. bond           : bond        0.00026 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 863.67 seconds
wall clock time: 15 minutes 31.06 seconds (931.06 seconds total)