Starting phenix.real_space_refine
on Wed Aug  5 13:10:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zi8_74265/08_2026/9zi8_74265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zi8_74265/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zi8_74265/08_2026/9zi8_74265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zi8_74265/08_2026/9zi8_74265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zi8_74265/08_2026/9zi8_74265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zi8_74265/08_2026/9zi8_74265.cif"
  }
  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-2.2rc3-6140/lib/python3.11/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: 2.35, per 1000 atoms: 0.24
  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: 0.55
  Conformation dependent library (CDL) restraints added in 50.1 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: 1.52
  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: 2.32

  Time building geometry restraints manager: 0.82 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=" N1    U A 264 "
       pdb=" C2    U A 264 "
    ideal  model  delta    sigma   weight residual
    1.381  1.402 -0.021 9.00e-03 1.23e+04 5.61e+00
  bond pdb=" N1    C A 318 "
       pdb=" C2    C A 318 "
    ideal  model  delta    sigma   weight residual
    1.397  1.377  0.020 1.00e-02 1.00e+04 4.11e+00
  bond pdb=" N9    G A 372 "
       pdb=" C4    G A 372 "
    ideal  model  delta    sigma   weight residual
    1.375  1.390 -0.015 8.00e-03 1.56e+04 3.51e+00
  bond pdb=" N9    A A 374 "
       pdb=" C4    A A 374 "
    ideal  model  delta    sigma   weight residual
    1.374  1.384 -0.010 6.00e-03 2.78e+04 2.86e+00
  bond pdb=" N9    A A 189 "
       pdb=" C4    A A 189 "
    ideal  model  delta    sigma   weight residual
    1.374  1.384 -0.010 6.00e-03 2.78e+04 2.59e+00
  ... (remaining 10995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 16082
        2.25 -     4.49: 832
        4.49 -     6.74: 26
        6.74 -     8.98: 3
        8.98 -    11.23: 1
  Bond angle restraints: 16944
  Sorted by residual:
  angle pdb=" N1    C A 318 "
        pdb=" C2    C A 318 "
        pdb=" O2    C A 318 "
      ideal   model   delta    sigma   weight residual
     118.90  114.88    4.02 6.00e-01 2.78e+00 4.50e+01
  angle pdb=" C1'   C A 318 "
        pdb=" N1    C A 318 "
        pdb=" C2    C A 318 "
      ideal   model   delta    sigma   weight residual
     118.80  111.56    7.24 1.10e+00 8.26e-01 4.33e+01
  angle pdb=" N1    U A 264 "
        pdb=" C2    U A 264 "
        pdb=" O2    U A 264 "
      ideal   model   delta    sigma   weight residual
     122.80  127.32   -4.52 7.00e-01 2.04e+00 4.17e+01
  angle pdb=" C1'   C A 318 "
        pdb=" N1    C A 318 "
        pdb=" C6    C A 318 "
      ideal   model   delta    sigma   weight residual
     120.80  128.40   -7.60 1.20e+00 6.94e-01 4.01e+01
  angle pdb=" O2    U A 264 "
        pdb=" C2    U A 264 "
        pdb=" N3    U A 264 "
      ideal   model   delta    sigma   weight residual
     122.20  117.77    4.43 7.00e-01 2.04e+00 4.00e+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: 1589
       0.047 -    0.094: 194
       0.094 -    0.140: 407
       0.140 -    0.187: 26
       0.187 -    0.234: 5
  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=" 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      2.47    2.26    0.22 2.00e-01 2.50e+01 1.17e+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
  ... (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:                  0.000
  Normalize map: mean=0, sd=1:             9.340
  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:          0.390
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.220
  Find NCS groups from input model:        0.040
  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:1.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
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      :  0.003   0.042  11000  Z= 0.255
  Angle     :  0.864  11.231  16944  Z= 0.734
  Chirality :  0.064   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        0.00281 /  0.25 (11000)
  covalent geometry    : angle       0.86394 /  0.73 (16944)
  hydrogen bonds       : bond        0.08866 /  8.87 (  404)
  hydrogen bonds       : angle       3.31715 /  4.06 (  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  : 0.117 
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: 0.0746
  time to fit residues: 3.1131
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  : 0.138 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:   50.0000
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   overall best weight:    7.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.089908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.050980 restraints weight = 55908.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.78
r_work: 0.2706 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.083  11000  Z= 0.548
  Angle     :  1.041  13.093  16944  Z= 0.516
  Chirality :  0.070   0.359   2221
  Planarity :  0.007   0.037    581
  Dihedral  : 25.773 166.446   6645
  Min Nonbonded Distance : 1.731

Molprobity Statistics.
  All-atom Clashscore : 25.35
  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: -0.62 (0.76), residues: 114
  helix:  0.90 (0.75), residues: 47
  sheet: -0.15 (0.87), residues: 28
  loop : -2.25 (0.95), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  57 
 TYR   0.021   0.004   TYR B  31 
 PHE   0.031   0.005   PHE B  13 
 HIS   0.004   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00848 /  0.55 (11000)
  covalent geometry    : angle       1.04143 /  0.52 (16944)
  hydrogen bonds       : bond        0.13987 / 14.05 (  404)
  hydrogen bonds       : angle       3.25780 /  4.00 (  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
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9340 (mp0) cc_final: 0.8980 (mp0)
REVERT: B   86 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7803 (mtm-85)
  outliers start: 7
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0795
  time to fit residues: 3.1500
Evaluate side-chains
  25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   86 ARG
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:   40.0000
   chunk 18 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    4.7386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.090360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.053142 restraints weight = 55789.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.63
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11000  Z= 0.331
  Angle     :  0.774  10.663  16944  Z= 0.409
  Chirality :  0.053   0.350   2221
  Planarity :  0.005   0.034    581
  Dihedral  : 25.857 166.726   6645
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 21.02
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.65 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 37.37 %
    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: -0.19 (0.80), residues: 114
  helix:  1.80 (0.81), residues: 44
  sheet: -0.69 (0.83), residues: 31
  loop : -1.90 (1.01), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   6 
 TYR   0.023   0.003   TYR B  40 
 PHE   0.021   0.004   PHE B  13 
 HIS   0.003   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.33 (11000)
  covalent geometry    : angle       0.77381 /  0.41 (16944)
  hydrogen bonds       : bond        0.10838 / 10.57 (  404)
  hydrogen bonds       : angle       2.90953 /  3.66 (  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
  27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9303 (mp0) cc_final: 0.8922 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 26
  average time/residue: 0.0609
  time to fit residues: 2.5471
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  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   97 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:   50.0000
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:   40.0000
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:   50.0000
   chunk 17 optimal weight:   30.0000
   overall best weight:    4.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.090121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.052978 restraints weight = 56751.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.64
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  11000  Z= 0.348
  Angle     :  0.772  11.129  16944  Z= 0.411
  Chirality :  0.052   0.381   2221
  Planarity :  0.006   0.036    581
  Dihedral  : 25.920 165.756   6645
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 22.18
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 27.27 %
    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:  0.18 (0.85), residues: 114
  helix:  1.53 (0.81), residues: 44
  sheet:  0.10 (0.88), residues: 29
  loop : -1.42 (1.19), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  35 
 TYR   0.016   0.002   TYR B  31 
 PHE   0.027   0.005   PHE B  13 
 HIS   0.006   0.004   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00555 /  0.35 (11000)
  covalent geometry    : angle       0.77202 /  0.41 (16944)
  hydrogen bonds       : bond        0.10921 / 10.57 (  404)
  hydrogen bonds       : angle       2.85538 /  3.60 (  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
  35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: B    5 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8274 (m-10)
REVERT: B   12 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8910 (mp0)
REVERT: B   18 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8687 (mm110)
REVERT: B   23 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8081 (m)
  outliers start: 11
  outliers final: 6
  residues processed: 30
  average time/residue: 0.0650
  time to fit residues: 3.0317
Evaluate side-chains
  34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 25
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
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   21 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   40 TYR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   97 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 16 optimal weight:   50.0000
   chunk 37 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 22 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 19 optimal weight:   40.0000
   chunk 2 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    9.7994

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.087996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.050131 restraints weight = 52245.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 3.20
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8957
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.102  11000  Z= 0.693
  Angle     :  1.273  15.069  16944  Z= 0.601
  Chirality :  0.083   0.427   2221
  Planarity :  0.007   0.036    581
  Dihedral  : 26.198 165.917   6645
  Min Nonbonded Distance : 1.635

Molprobity Statistics.
  All-atom Clashscore : 32.99
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  Rotamer:
    Outliers : 12.12 %
    Allowed  : 30.30 %
    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: -1.13 (0.80), residues: 114
  helix:  0.22 (0.75), residues: 47
  sheet: -0.90 (0.80), residues: 29
  loop : -1.69 (1.19), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   6 
 TYR   0.026   0.004   TYR B  31 
 PHE   0.028   0.006   PHE B  13 
 HIS   0.007   0.005   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01092 /  0.69 (11000)
  covalent geometry    : angle       1.27287 /  0.60 (16944)
  hydrogen bonds       : bond        0.16069 / 15.96 (  404)
  hydrogen bonds       : angle       3.49865 /  4.45 (  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
  34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 22
  time to evaluate  : 0.097 
Fit side-chains
REVERT: B    9 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8378 (mtmm)
REVERT: B   12 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8950 (mp0)
REVERT: B   18 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8785 (mm110)
REVERT: B   23 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (m)
REVERT: B   86 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7872 (mtm-85)
  outliers start: 12
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0758
  time to fit residues: 3.2413
Evaluate side-chains
  32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   40 TYR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 ARG
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 22 optimal weight:   50.0000
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:   40.0000
   chunk 42 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.8984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.090527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.053787 restraints weight = 57022.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.46
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11000  Z= 0.193
  Angle     :  0.655  10.443  16944  Z= 0.371
  Chirality :  0.043   0.378   2221
  Planarity :  0.005   0.039    581
  Dihedral  : 26.062 166.356   6645
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  7.89 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 41.41 %
    Favored  : 55.56 %
  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:  0.47 (0.88), residues: 114
  helix:  2.50 (0.84), residues: 44
  sheet: -0.72 (0.81), residues: 31
  loop : -1.37 (1.24), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  35 
 TYR   0.012   0.002   TYR B  31 
 PHE   0.015   0.002   PHE B  28 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.19 (11000)
  covalent geometry    : angle       0.65548 /  0.37 (16944)
  hydrogen bonds       : bond        0.09311 /  8.92 (  404)
  hydrogen bonds       : angle       2.70630 /  3.35 (  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
  31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   12 GLU cc_start: 0.9206 (mp0) cc_final: 0.8816 (mp0)
REVERT: B   18 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8684 (mm110)
  outliers start: 3
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0662
  time to fit residues: 3.0218
Evaluate side-chains
  28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:   10.9990
   chunk 26 optimal weight:   10.0000
   chunk 22 optimal weight:   50.0000
   chunk 3 optimal weight:   20.0000
   chunk 12 optimal weight:   40.0000
   chunk 18 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:   40.0000
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   overall best weight:    9.9996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.087565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.047371 restraints weight = 52584.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 2.23
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.095  11000  Z= 0.699
  Angle     :  1.270  16.235  16944  Z= 0.597
  Chirality :  0.083   0.409   2221
  Planarity :  0.007   0.040    581
  Dihedral  : 26.185 165.158   6645
  Min Nonbonded Distance : 1.653

Molprobity Statistics.
  All-atom Clashscore : 34.09
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.40 %
    Favored  : 87.72 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 33.33 %
    Favored  : 55.56 %
  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: -1.31 (0.79), residues: 114
  helix:  0.33 (0.75), residues: 47
  sheet: -1.41 (0.76), residues: 31
  loop : -1.75 (1.20), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   6 
 TYR   0.026   0.004   TYR B  31 
 PHE   0.026   0.007   PHE B  13 
 HIS   0.011   0.007   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01113 /  0.70 (11000)
  covalent geometry    : angle       1.27032 /  0.60 (16944)
  hydrogen bonds       : bond        0.15920 / 15.83 (  404)
  hydrogen bonds       : angle       3.43398 /  4.53 (  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
  33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 22
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B    9 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8480 (mtmm)
REVERT: B   18 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8797 (mm110)
  outliers start: 11
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0877
  time to fit residues: 3.8460
Evaluate side-chains
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   40 TYR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 41 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 34 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    6.9788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.088612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.049941 restraints weight = 56544.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.67
r_work: 0.2724 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082  11000  Z= 0.499
  Angle     :  1.005  10.961  16944  Z= 0.500
  Chirality :  0.067   0.369   2221
  Planarity :  0.006   0.036    581
  Dihedral  : 26.234 165.166   6645
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 29.62
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 37.37 %
    Favored  : 55.56 %
  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: -0.97 (0.81), residues: 114
  helix:  0.77 (0.75), residues: 46
  sheet: -1.57 (0.75), residues: 31
  loop : -1.43 (1.25), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   6 
 TYR   0.017   0.003   TYR B  31 
 PHE   0.016   0.004   PHE B  28 
 HIS   0.008   0.005   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00813 /  0.50 (11000)
  covalent geometry    : angle       1.00517 /  0.50 (16944)
  hydrogen bonds       : bond        0.13185 / 12.83 (  404)
  hydrogen bonds       : angle       3.07466 /  4.06 (  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
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B    9 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8176 (mtmm)
REVERT: B   12 GLU cc_start: 0.9297 (mp0) cc_final: 0.8968 (mp0)
REVERT: B   18 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8844 (mm110)
REVERT: B   87 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9080 (tm-30)
  outliers start: 7
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0858
  time to fit residues: 3.4907
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 47 optimal weight:    0.5980
   chunk 12 optimal weight:   40.0000
   chunk 39 optimal weight:    7.9990
   chunk 13 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 51 optimal weight:    0.1980
   chunk 50 optimal weight:    0.6980
   chunk 1 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    2.6984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.090008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.053522 restraints weight = 56729.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.45
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11000  Z= 0.211
  Angle     :  0.635  10.176  16944  Z= 0.366
  Chirality :  0.042   0.311   2221
  Planarity :  0.005   0.036    581
  Dihedral  : 26.100 165.779   6645
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.65 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 40.40 %
    Favored  : 56.57 %
  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:  0.40 (0.89), residues: 114
  helix:  2.33 (0.85), residues: 43
  sheet: -0.91 (0.81), residues: 31
  loop : -0.99 (1.27), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  65 
 TYR   0.009   0.002   TYR B  81 
 PHE   0.011   0.002   PHE B  13 
 HIS   0.003   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.21 (11000)
  covalent geometry    : angle       0.63532 /  0.37 (16944)
  hydrogen bonds       : bond        0.09184 /  8.75 (  404)
  hydrogen bonds       : angle       2.67944 /  3.47 (  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
  30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B   11 GLU cc_start: 0.8697 (mp0) cc_final: 0.8482 (mp0)
REVERT: B   12 GLU cc_start: 0.9214 (mp0) cc_final: 0.8918 (mp0)
REVERT: B   18 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8656 (mm110)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0757
  time to fit residues: 3.3496
Evaluate side-chains
  28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
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:   30.0000
   chunk 50 optimal weight:    0.9990
   chunk 22 optimal weight:   50.0000
   chunk 46 optimal weight:    0.5980
   chunk 35 optimal weight:   30.0000
   chunk 21 optimal weight:   50.0000
   chunk 2 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:   50.0000
   overall best weight:    6.1190

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.088803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.049506 restraints weight = 55863.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.60
r_work: 0.2753 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8997
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  11000  Z= 0.442
  Angle     :  0.873  10.111  16944  Z= 0.451
  Chirality :  0.059   0.311   2221
  Planarity :  0.006   0.036    581
  Dihedral  : 26.119 164.286   6645
  Min Nonbonded Distance : 1.761

Molprobity Statistics.
  All-atom Clashscore : 27.04
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 37.37 %
    Favored  : 56.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.86), residues: 114
  helix:  1.34 (0.79), residues: 46
  sheet: -1.23 (0.77), residues: 31
  loop : -0.97 (1.37), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  65 
 TYR   0.017   0.002   TYR B  31 
 PHE   0.023   0.005   PHE B  28 
 HIS   0.007   0.005   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00701 /  0.44 (11000)
  covalent geometry    : angle       0.87255 /  0.45 (16944)
  hydrogen bonds       : bond        0.12230 / 11.94 (  404)
  hydrogen bonds       : angle       2.96287 /  3.90 (  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
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.140 
Fit side-chains
REVERT: B    9 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8388 (tppp)
REVERT: B   18 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8800 (mm110)
  outliers start: 6
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0897
  time to fit residues: 3.6117
Evaluate side-chains
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   60 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:    7.9990
   chunk 16 optimal weight:   50.0000
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:   20.0000
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:   40.0000
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.7584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.090334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.052300 restraints weight = 57335.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.09
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11000  Z= 0.163
  Angle     :  0.602   9.721  16944  Z= 0.349
  Chirality :  0.040   0.282   2221
  Planarity :  0.005   0.036    581
  Dihedral  : 26.036 167.207   6645
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 20.37
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  9.65 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 38.38 %
    Favored  : 55.56 %
  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:  0.77 (0.90), residues: 114
  helix:  2.60 (0.87), residues: 43
  sheet: -0.59 (0.83), residues: 31
  loop : -0.86 (1.27), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  65 
 TYR   0.009   0.002   TYR B  81 
 PHE   0.009   0.002   PHE B  28 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.16 (11000)
  covalent geometry    : angle       0.60206 /  0.35 (16944)
  hydrogen bonds       : bond        0.08508 /  8.18 (  404)
  hydrogen bonds       : angle       2.63920 /  3.40 (  752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3206.81 seconds
wall clock time: 55 minutes 25.45 seconds (3325.45 seconds total)