Starting phenix.real_space_refine
on Thu Jun  4 02:31:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zi8_74265/06_2026/9zi8_74265.map"
  }
  resolution = 3.18
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     417      5.49       5
     Mg     34      5.21       5
     S       3      5.16       5
     C    4604      2.51       5
     N    1834      2.21       5
     O    3051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9943
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 8962
          Classifications: {'RNA': 417}
          Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 16, 'rna3p_pur': 220, 'rna3p_pyr': 158}
          Link IDs: {'rna2p': 39, 'rna3p': 377}
    Chain: "B"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 947
          Classifications: {'peptide': 116}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 34
          Unusual residues: {' MG': 34}
          Classifications: {'undetermined': 34}
          Link IDs: {None: 33}
  Time building chain proxies: 2.46, per 1000 atoms: 0.25
  Number of scatterers: 9943
  At special positions: 0
  Unit cell: (125.172, 171.288, 142.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       3     16.00
     P     417     15.00
     Mg     34     11.99
     O    3051      8.00
     N    1834      7.00
     C    4604      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=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 47.5 milliseconds
  

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  216

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 1 sheets defined
      46.6% alpha, 18.1% beta
      139 base pairs and 217 stacking pairs defined.
    Time for finding SS restraints: 1.75
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 19
    Processing helix  chain 'B' and resid 49 through 52
      removed outlier: 4.032A  pdb=" N   GLY B  52 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 49 through 52'
    Processing helix  chain 'B' and resid 53 through 71
    Processing helix  chain 'B' and resid 87 through 90
    Processing helix  chain 'B' and resid 93 through 108
      removed outlier: 3.769A  pdb=" N   LYS B 107 " --> pdb=" O   HIS B 103 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 25
      removed outlier: 3.585A  pdb=" N   PHE B  28 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B  42 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA B  85 " --> pdb=" O   SER B  46 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    138 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      356 hydrogen bonds
      614 hydrogen bond angles
      0 basepair planarities
      139 basepair parallelities
      217 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1101
        1.33 -     1.45: 5386
        1.45 -     1.57: 3675
        1.57 -     1.69: 833
        1.69 -     1.81: 5
  Bond restraints: 11000
  Sorted by residual:
  bond pdb=" CB  GLU B  91 "
       pdb=" CG  GLU B  91 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.98e+00
  bond pdb=" CB  GLU B  37 "
       pdb=" CG  GLU B  37 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.91e+00
  bond pdb=" CG  GLU B  15 "
       pdb=" CD  GLU B  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.66e+00
  bond pdb=" C3'   U A 126 "
       pdb=" O3'   U A 126 "
    ideal  model  delta    sigma   weight residual
    1.427  1.445 -0.018 1.50e-02 4.44e+03 1.38e+00
  bond pdb=" C3'   G A  32 "
       pdb=" O3'   G A  32 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.29e+00
  ... (remaining 10995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 16753
        2.25 -     4.49: 162
        4.49 -     6.74: 25
        6.74 -     8.98: 3
        8.98 -    11.23: 1
  Bond angle restraints: 16944
  Sorted by residual:
  angle pdb=" O3'   G A  32 "
        pdb=" P     U A  33 "
        pdb=" OP1   U A  33 "
      ideal   model   delta    sigma   weight residual
     108.00  119.23  -11.23 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" C3'   G A  32 "
        pdb=" O3'   G A  32 "
        pdb=" P     U A  33 "
      ideal   model   delta    sigma   weight residual
     120.20  125.73   -5.53 1.50e+00 4.44e-01 1.36e+01
  angle pdb=" C3'   U A 185 "
        pdb=" O3'   U A 185 "
        pdb=" P     G A 186 "
      ideal   model   delta    sigma   weight residual
     120.20  125.48   -5.28 1.50e+00 4.44e-01 1.24e+01
  angle pdb=" CB  GLU B  37 "
        pdb=" CG  GLU B  37 "
        pdb=" CD  GLU B  37 "
      ideal   model   delta    sigma   weight residual
     112.60  118.37   -5.77 1.70e+00 3.46e-01 1.15e+01
  angle pdb=" O4'   G A 172 "
        pdb=" C1'   G A 172 "
        pdb=" N9    G A 172 "
      ideal   model   delta    sigma   weight residual
     108.20  113.26   -5.06 1.50e+00 4.44e-01 1.14e+01
  ... (remaining 16939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.05: 5906
       33.05 -    66.09: 1049
       66.09 -    99.14: 150
       99.14 -   132.19: 5
      132.19 -   165.23: 6
  Dihedral angle restraints: 7116
    sinusoidal: 6779
      harmonic: 337
  Sorted by residual:
  dihedral pdb=" O4'   U A 180 "
           pdb=" C1'   U A 180 "
           pdb=" N1    U A 180 "
           pdb=" C2    U A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   39.85  160.15     1      1.50e+01 4.44e-03 8.28e+01
  dihedral pdb=" O4'   U A 267 "
           pdb=" C1'   U A 267 "
           pdb=" N1    U A 267 "
           pdb=" C2    U A 267 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.54  155.46     1      1.50e+01 4.44e-03 8.15e+01
  dihedral pdb=" O4'   U A 264 "
           pdb=" C1'   U A 264 "
           pdb=" N1    U A 264 "
           pdb=" C2    U A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  148.36   83.64     1      1.70e+01 3.46e-03 2.95e+01
  ... (remaining 7113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 2043
       0.047 -    0.094: 130
       0.094 -    0.140: 37
       0.140 -    0.187: 7
       0.187 -    0.234: 4
  Chirality restraints: 2221
  Sorted by residual:
  chirality pdb=" P     U A  33 "
            pdb=" OP1   U A  33 "
            pdb=" OP2   U A  33 "
            pdb=" O5'   U A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.64   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C3'   U A 171 "
            pdb=" C4'   U A 171 "
            pdb=" O3'   U A 171 "
            pdb=" C2'   U A 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.26   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" C1'   G A 234 "
            pdb=" O4'   G A 234 "
            pdb=" C2'   G A 234 "
            pdb=" N9    G A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.26    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 2218 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  32 "   -0.038 2.00e-02 2.50e+03   1.66e-02 8.29e+00
        pdb=" N9    G A  32 "    0.041 2.00e-02 2.50e+03
        pdb=" C8    G A  32 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    G A  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G A  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A  32 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G A  32 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G A  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G A  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G A  32 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    G A  32 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G A  32 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 231 "    0.035 2.00e-02 2.50e+03   1.53e-02 6.48e+00
        pdb=" N9    A A 231 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8    A A 231 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    A A 231 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A A 231 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A A 231 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A A 231 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A A 231 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    A A 231 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    A A 231 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A A 231 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 298 "    0.032 2.00e-02 2.50e+03   1.40e-02 5.90e+00
        pdb=" N9    G A 298 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8    G A 298 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G A 298 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 298 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 298 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6    G A 298 "    0.011 2.00e-02 2.50e+03
        pdb=" N1    G A 298 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 298 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G A 298 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    G A 298 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G A 298 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 35
        2.53 -     3.12: 6881
        3.12 -     3.71: 20974
        3.71 -     4.31: 27810
        4.31 -     4.90: 34942
  Nonbonded interactions: 90642
  Sorted by model distance:
  nonbonded pdb=" OP1   A A 257 "
            pdb="MG    MG A 509 "
     model   vdw
     1.935 2.170
  nonbonded pdb=" OP2   G A 331 "
            pdb="MG    MG A 512 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" OP2   A A 390 "
            pdb="MG    MG A 505 "
     model   vdw
     1.987 2.170
  nonbonded pdb=" OP2   C A 258 "
            pdb="MG    MG A 509 "
     model   vdw
     2.014 2.170
  nonbonded pdb=" OP1   G A 275 "
            pdb="MG    MG A 513 "
     model   vdw
     2.025 2.170
  ... (remaining 90637 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             8.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
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      :  0.002   0.042  11000  Z= 0.130
  Angle     :  0.594  11.231  16944  Z= 0.300
  Chirality :  0.030   0.234   2221
  Planarity :  0.004   0.030    581
  Dihedral  : 25.508 165.232   6900
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  6.14 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.29 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.82), residues: 114
  helix:  2.46 (0.83), residues: 44
  sheet:  0.76 (0.98), residues: 28
  loop : -2.20 (0.87), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  59 
 TYR   0.023   0.002   TYR B   5 
 PHE   0.008   0.002   PHE B  68 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.13 (11000)
  covalent geometry    : angle       0.59395 /  0.30 (16944)
  hydrogen bonds       : bond        0.08866 /  5.08 (  404)
  hydrogen bonds       : angle       3.31715 /  2.17 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9018 (mp0) cc_final: 0.8749 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0792
  time to fit residues: 3.2512
Evaluate side-chains
  25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.088955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.051018 restraints weight = 52514.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 2.74
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.056  11000  Z= 0.477
  Angle     :  0.842  10.230  16944  Z= 0.414
  Chirality :  0.044   0.269   2221
  Planarity :  0.005   0.031    581
  Dihedral  : 25.990 166.030   6645
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 21.47
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  6.14 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 32.32 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.81), residues: 114
  helix:  1.97 (0.82), residues: 44
  sheet:  0.53 (0.94), residues: 28
  loop : -1.94 (0.93), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  35 
 TYR   0.013   0.002   TYR B  31 
 PHE   0.024   0.004   PHE B  68 
 HIS   0.004   0.003   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00894 /  0.48 (11000)
  covalent geometry    : angle       0.84167 /  0.41 (16944)
  hydrogen bonds       : bond        0.10045 /  5.95 (  404)
  hydrogen bonds       : angle       2.63780 /  1.75 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9111 (mp0) cc_final: 0.8791 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0770
  time to fit residues: 3.0599
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  104 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.091616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.055160 restraints weight = 56567.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.53
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11000  Z= 0.187
  Angle     :  0.616  10.779  16944  Z= 0.309
  Chirality :  0.033   0.218   2221
  Planarity :  0.004   0.024    581
  Dihedral  : 25.745 164.675   6645
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.26 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 36.36 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.82), residues: 114
  helix:  2.72 (0.85), residues: 43
  sheet:  1.00 (0.91), residues: 26
  loop : -2.03 (0.87), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 106 
 TYR   0.008   0.001   TYR B  31 
 PHE   0.012   0.002   PHE B  13 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.19 (11000)
  covalent geometry    : angle       0.61598 /  0.31 (16944)
  hydrogen bonds       : bond        0.06653 /  3.98 (  404)
  hydrogen bonds       : angle       2.39703 /  1.61 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.148 
Fit side-chains
REVERT: B    3 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8667 (mtmt)
REVERT: B   12 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8914 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0962
  time to fit residues: 4.0099
Evaluate side-chains
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 LYS
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:   20.0000
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:   30.0000
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.090278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.050791 restraints weight = 56909.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.30
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11000  Z= 0.326
  Angle     :  0.694   9.798  16944  Z= 0.346
  Chirality :  0.037   0.235   2221
  Planarity :  0.004   0.023    581
  Dihedral  : 25.810 165.347   6645
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  7.89 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 32.32 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.81), residues: 114
  helix:  2.46 (0.83), residues: 43
  sheet:  0.20 (0.91), residues: 28
  loop : -2.07 (0.91), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   6 
 TYR   0.011   0.002   TYR B  31 
 PHE   0.017   0.003   PHE B  13 
 HIS   0.003   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00611 /  0.33 (11000)
  covalent geometry    : angle       0.69367 /  0.35 (16944)
  hydrogen bonds       : bond        0.07893 /  4.70 (  404)
  hydrogen bonds       : angle       2.48246 /  1.64 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B    3 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8717 (mtmt)
REVERT: B  112 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7576 (mtmm)
  outliers start: 7
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1030
  time to fit residues: 4.4415
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 LYS
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 37 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 22 optimal weight:   40.0000
   chunk 11 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.087964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.050585 restraints weight = 52445.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.70
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.060  11000  Z= 0.479
  Angle     :  0.847   8.929  16944  Z= 0.417
  Chirality :  0.044   0.256   2221
  Planarity :  0.005   0.024    581
  Dihedral  : 26.119 170.130   6645
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 23.28
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  8.08 %
    Allowed  : 34.34 %
    Favored  : 57.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.81), residues: 114
  helix:  2.02 (0.80), residues: 46
  sheet: -0.35 (0.83), residues: 29
  loop : -1.89 (1.02), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  57 
 TYR   0.017   0.003   TYR B  40 
 PHE   0.016   0.004   PHE B  13 
 HIS   0.005   0.004   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00901 /  0.48 (11000)
  covalent geometry    : angle       0.84686 /  0.42 (16944)
  hydrogen bonds       : bond        0.09982 /  5.91 (  404)
  hydrogen bonds       : angle       2.67890 /  1.76 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B    3 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8992 (mtmt)
REVERT: B   12 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8826 (mp0)
REVERT: B   43 ILE cc_start: 0.9089 (mm) cc_final: 0.8839 (tt)
REVERT: B  112 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7441 (mtmm)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 0.0975
  time to fit residues: 4.0829
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 LYS
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   40 TYR
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:   40.0000
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.091070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.053143 restraints weight = 57412.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.21
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11000  Z= 0.136
  Angle     :  0.605   8.732  16944  Z= 0.303
  Chirality :  0.031   0.220   2221
  Planarity :  0.004   0.022    581
  Dihedral  : 25.771 171.470   6645
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.26 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 34.34 %
    Favored  : 59.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.83), residues: 114
  helix:  2.95 (0.85), residues: 43
  sheet:  0.60 (0.88), residues: 26
  loop : -1.85 (0.93), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  57 
 TYR   0.007   0.001   TYR B  81 
 PHE   0.011   0.002   PHE B  13 
 HIS   0.000   0.000   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.14 (11000)
  covalent geometry    : angle       0.60510 /  0.30 (16944)
  hydrogen bonds       : bond        0.06567 /  3.93 (  404)
  hydrogen bonds       : angle       2.37707 /  1.57 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.118 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8689 (mp0)
REVERT: B   43 ILE cc_start: 0.9054 (mm) cc_final: 0.8661 (pt)
REVERT: B  112 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7094 (mtmm)
  outliers start: 6
  outliers final: 3
  residues processed: 29
  average time/residue: 0.0949
  time to fit residues: 4.0563
Evaluate side-chains
  31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:   40.0000
   chunk 3 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.087618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.052241 restraints weight = 52635.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.54
r_work: 0.2715 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.065  11000  Z= 0.533
  Angle     :  0.866   8.655  16944  Z= 0.425
  Chirality :  0.045   0.264   2221
  Planarity :  0.005   0.021    581
  Dihedral  : 26.073 169.330   6645
  Min Nonbonded Distance : 1.761

Molprobity Statistics.
  All-atom Clashscore : 23.48
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.65 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 32.32 %
    Favored  : 61.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.83), residues: 114
  helix:  1.98 (0.81), residues: 46
  sheet: -0.70 (0.83), residues: 31
  loop : -1.75 (1.11), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  57 
 TYR   0.013   0.002   TYR B  81 
 PHE   0.019   0.004   PHE B  13 
 HIS   0.006   0.004   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01003 /  0.53 (11000)
  covalent geometry    : angle       0.86628 /  0.43 (16944)
  hydrogen bonds       : bond        0.10420 /  6.16 (  404)
  hydrogen bonds       : angle       2.68951 /  1.73 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B    5 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8575 (m-10)
REVERT: B   12 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8978 (mp0)
REVERT: B  112 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (mtmm)
  outliers start: 6
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0863
  time to fit residues: 3.2804
Evaluate side-chains
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 TYR
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.089115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.052215 restraints weight = 51811.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.41
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11000  Z= 0.247
  Angle     :  0.658   8.169  16944  Z= 0.329
  Chirality :  0.035   0.230   2221
  Planarity :  0.004   0.028    581
  Dihedral  : 25.910 170.733   6645
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  8.77 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 36.36 %
    Favored  : 58.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.83), residues: 114
  helix:  2.81 (0.86), residues: 43
  sheet: -0.21 (0.82), residues: 29
  loop : -1.79 (0.96), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 106 
 TYR   0.010   0.002   TYR B  31 
 PHE   0.011   0.002   PHE B  28 
 HIS   0.002   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.25 (11000)
  covalent geometry    : angle       0.65796 /  0.33 (16944)
  hydrogen bonds       : bond        0.07374 /  4.38 (  404)
  hydrogen bonds       : angle       2.43169 /  1.60 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8807 (mp0)
REVERT: B   74 GLU cc_start: 0.8334 (tp30) cc_final: 0.8130 (tp30)
REVERT: B  112 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7196 (mtmm)
  outliers start: 5
  outliers final: 3
  residues processed: 29
  average time/residue: 0.0844
  time to fit residues: 3.7252
Evaluate side-chains
  32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 12 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.091032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.054966 restraints weight = 57012.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.40
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11000  Z= 0.164
  Angle     :  0.588   7.708  16944  Z= 0.295
  Chirality :  0.031   0.225   2221
  Planarity :  0.004   0.025    581
  Dihedral  : 25.634 170.106   6645
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  6.14 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 35.35 %
    Favored  : 59.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.82), residues: 114
  helix:  3.00 (0.87), residues: 43
  sheet:  0.77 (0.87), residues: 26
  loop : -1.87 (0.89), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  35 
 TYR   0.009   0.001   TYR B  81 
 PHE   0.010   0.002   PHE B  28 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.16 (11000)
  covalent geometry    : angle       0.58849 /  0.30 (16944)
  hydrogen bonds       : bond        0.06629 /  3.96 (  404)
  hydrogen bonds       : angle       2.35381 /  1.54 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8755 (mp0)
REVERT: B   43 ILE cc_start: 0.9103 (mm) cc_final: 0.8740 (pt)
REVERT: B   74 GLU cc_start: 0.8293 (tp30) cc_final: 0.7972 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0870
  time to fit residues: 3.6925
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:   30.0000
   chunk 46 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:   50.0000
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:   30.0000
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.088600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.051539 restraints weight = 50681.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 1.62
r_work: 0.2716 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  11000  Z= 0.330
  Angle     :  0.697   7.535  16944  Z= 0.348
  Chirality :  0.037   0.233   2221
  Planarity :  0.004   0.027    581
  Dihedral  : 25.794 168.894   6645
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  7.89 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 33.33 %
    Favored  : 61.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.82), residues: 114
  helix:  2.75 (0.86), residues: 43
  sheet:  0.12 (0.83), residues: 29
  loop : -1.63 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  57 
 TYR   0.011   0.002   TYR B  31 
 PHE   0.014   0.003   PHE B  13 
 HIS   0.004   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00622 /  0.33 (11000)
  covalent geometry    : angle       0.69737 /  0.35 (16944)
  hydrogen bonds       : bond        0.08211 /  4.85 (  404)
  hydrogen bonds       : angle       2.47099 /  1.61 (  752)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.152 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9025 (mp0)
REVERT: B   74 GLU cc_start: 0.8663 (tp30) cc_final: 0.8248 (tp30)
  outliers start: 5
  outliers final: 4
  residues processed: 28
  average time/residue: 0.0881
  time to fit residues: 3.7544
Evaluate side-chains
  31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  112 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:   30.0000
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 43 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.090513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.056710 restraints weight = 57296.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.16
r_work: 0.2747 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11000  Z= 0.197
  Angle     :  0.602   7.432  16944  Z= 0.303
  Chirality :  0.032   0.227   2221
  Planarity :  0.004   0.027    581
  Dihedral  : 25.667 169.291   6645
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  6.14 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 35.35 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.83), residues: 114
  helix:  2.99 (0.87), residues: 43
  sheet:  0.76 (0.86), residues: 26
  loop : -1.75 (0.92), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B   6 
 TYR   0.009   0.001   TYR B  31 
 PHE   0.006   0.001   PHE B  13 
 HIS   0.002   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.20 (11000)
  covalent geometry    : angle       0.60243 /  0.30 (16944)
  hydrogen bonds       : bond        0.06878 /  4.09 (  404)
  hydrogen bonds       : angle       2.36262 /  1.56 (  752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3666.42 seconds
wall clock time: 63 minutes 20.54 seconds (3800.54 seconds total)