Starting phenix.real_space_refine
on Fri Oct 10 10:17:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwe_35765/10_2025/8iwe_35765_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    1497      2.51       5
     N     353      2.21       5
     O     374      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2236
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2226
          Classifications: {'peptide': 296}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 12, 'TRANS': 283}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 65
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'SPD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.77, per 1000 atoms: 0.34
  Number of scatterers: 2236
  At special positions: 0
  Unit cell: (63.403, 75.905, 75.012, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     374      8.00
     N     353      7.00
     C    1497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  22 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 144.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  562

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 0 sheets defined
      78.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'R' and resid 35 through 57
      removed outlier: 4.975A  pdb=" N   LEU R  41 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLY R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ASN R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL R  53 " --> pdb=" O   GLY R  49 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE R  55 " --> pdb=" O   LEU R  51 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA R  56 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 85
      removed outlier: 4.114A  pdb=" N   VAL R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R  81 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 96
    Processing helix  chain 'R' and resid 104 through 136
      removed outlier: 3.657A  pdb=" N   THR R 109 " --> pdb=" O   CYS R 105 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   CYS R 110 " --> pdb=" O   LYS R 106 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASP R 112 " --> pdb=" O   HIS R 108 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   THR R 113 " --> pdb=" O   THR R 109 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER R 114 " --> pdb=" O   CYS R 110 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE R 117 " --> pdb=" O   THR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
      removed outlier: 3.735A  pdb=" N   LYS R 143 " --> pdb=" O   THR R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 169
      removed outlier: 3.776A  pdb=" N   PHE R 158 " --> pdb=" O   ALA R 154 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER R 164 " --> pdb=" O   SER R 160 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER R 166 " --> pdb=" O   THR R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 232
      removed outlier: 4.340A  pdb=" N   LEU R 200 " --> pdb=" O   GLN R 196 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LEU R 201 " --> pdb=" O   ASN R 197 " (cutoff:3.500A)
      Proline residue:  R 209  - end of helix
      removed outlier: 3.991A  pdb=" N   VAL R 212 " --> pdb=" O   LEU R 208 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   MET R 213 " --> pdb=" O   PRO R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 246 through 283
      removed outlier: 4.395A  pdb=" N   LYS R 251 " --> pdb=" O   GLU R 247 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG R 252 " --> pdb=" O   ARG R 248 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR R 259 " --> pdb=" O   LYS R 255 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LEU R 260 " --> pdb=" O   ALA R 256 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA R 263 " --> pdb=" O   THR R 259 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 3.772A  pdb=" N   ALA R 282 " --> pdb=" O   ALA R 278 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR R 283 " --> pdb=" O   VAL R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 312
      removed outlier: 3.610A  pdb=" N   TYR R 293 " --> pdb=" O   PRO R 289 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ILE R 295 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL R 300 " --> pdb=" O   LEU R 296 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN R 303 " --> pdb=" O   CYS R 299 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   SER R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ALA R 305 " --> pdb=" O   TYR R 301 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 315 through 327

    144 hydrogen bonds defined for protein.
    432 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.30

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 346
        1.32 -     1.45: 686
        1.45 -     1.57: 1255
        1.57 -     1.69: 0
        1.69 -     1.81: 15
  Bond restraints: 2302
  Sorted by residual:
  bond pdb=" C   VAL R  94 "
       pdb=" O   VAL R  94 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.034 1.23e-02 6.61e+03 7.83e+00
  bond pdb=" CA  VAL R  94 "
       pdb=" CB  VAL R  94 "
    ideal  model  delta    sigma   weight residual
    1.540  1.510  0.030 1.37e-02 5.33e+03 4.72e+00
  bond pdb=" CA  ILE R 280 "
       pdb=" C   ILE R 280 "
    ideal  model  delta    sigma   weight residual
    1.519  1.542 -0.023 1.14e-02 7.69e+03 4.22e+00
  bond pdb=" CA  VAL R  94 "
       pdb=" C   VAL R  94 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 1.39e-02 5.18e+03 3.44e+00
  bond pdb=" CA  TYR R 302 "
       pdb=" C   TYR R 302 "
    ideal  model  delta    sigma   weight residual
    1.522  1.498  0.024 1.41e-02 5.03e+03 2.94e+00
  ... (remaining 2297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 2999
        1.92 -     3.85: 119
        3.85 -     5.77: 19
        5.77 -     7.70: 8
        7.70 -     9.62: 3
  Bond angle restraints: 3148
  Sorted by residual:
  angle pdb=" N   ASN R 303 "
        pdb=" CA  ASN R 303 "
        pdb=" C   ASN R 303 "
      ideal   model   delta    sigma   weight residual
     112.38  103.43    8.95 1.22e+00 6.72e-01 5.38e+01
  angle pdb=" N   ILE R 280 "
        pdb=" CA  ILE R 280 "
        pdb=" C   ILE R 280 "
      ideal   model   delta    sigma   weight residual
     113.07  122.36   -9.29 1.36e+00 5.41e-01 4.66e+01
  angle pdb=" C   TYR R 315 "
        pdb=" N   PRO R 316 "
        pdb=" CA  PRO R 316 "
      ideal   model   delta    sigma   weight residual
     119.84  126.85   -7.01 1.25e+00 6.40e-01 3.15e+01
  angle pdb=" N   PHE R 286 "
        pdb=" CA  PHE R 286 "
        pdb=" C   PHE R 286 "
      ideal   model   delta    sigma   weight residual
     111.54  119.15   -7.61 1.36e+00 5.41e-01 3.13e+01
  angle pdb=" N   PHE R 207 "
        pdb=" CA  PHE R 207 "
        pdb=" C   PHE R 207 "
      ideal   model   delta    sigma   weight residual
     111.36  116.49   -5.13 1.09e+00 8.42e-01 2.21e+01
  ... (remaining 3143 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.82: 1053
       11.82 -    23.64: 149
       23.64 -    35.45: 63
       35.45 -    47.27: 30
       47.27 -    59.09: 11
  Dihedral angle restraints: 1306
    sinusoidal: 434
      harmonic: 872
  Sorted by residual:
  dihedral pdb=" C   VAL R 279 "
           pdb=" N   VAL R 279 "
           pdb=" CA  VAL R 279 "
           pdb=" CB  VAL R 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.52   15.52     0      2.50e+00 1.60e-01 3.85e+01
  dihedral pdb=" N   VAL R 279 "
           pdb=" C   VAL R 279 "
           pdb=" CA  VAL R 279 "
           pdb=" CB  VAL R 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  133.59  -10.19     0      2.50e+00 1.60e-01 1.66e+01
  dihedral pdb=" N   TRP R 317 "
           pdb=" C   TRP R 317 "
           pdb=" CA  TRP R 317 "
           pdb=" CB  TRP R 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.73   -7.93     0      2.50e+00 1.60e-01 1.01e+01
  ... (remaining 1303 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 334
       0.090 -    0.180: 22
       0.180 -    0.269: 6
       0.269 -    0.359: 2
       0.359 -    0.449: 2
  Chirality restraints: 366
  Sorted by residual:
  chirality pdb=" CA  VAL R 279 "
            pdb=" N   VAL R 279 "
            pdb=" C   VAL R 279 "
            pdb=" CB  VAL R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.99    0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CA  PHE R 286 "
            pdb=" N   PHE R 286 "
            pdb=" C   PHE R 286 "
            pdb=" CB  PHE R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CA  TRP R 317 "
            pdb=" N   TRP R 317 "
            pdb=" C   TRP R 317 "
            pdb=" CB  TRP R 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 363 not shown)

  Planarity restraints: 385
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 301 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.25e+00
        pdb=" C   TYR R 301 "    0.053 2.00e-02 2.50e+03
        pdb=" O   TYR R 301 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR R 302 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 147 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   SER R 147 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   SER R 147 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL R 148 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R  95 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   GLU R  95 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLU R  95 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER R  96 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 382 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 798
        2.84 -     3.35: 2124
        3.35 -     3.87: 3444
        3.87 -     4.38: 3753
        4.38 -     4.90: 6479
  Nonbonded interactions: 16598
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 112 "
            pdb=" OH  TYR R 301 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OD2 ASP R 281 "
            pdb=" OG1 THR R 288 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" O   THR R 109 "
            pdb=" OG1 THR R 113 "
     model   vdw
     2.422 3.040
  nonbonded pdb=" O   ASP R 281 "
            pdb=" O   MET R 284 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   THR R 139 "
            pdb=" OG1 THR R 139 "
     model   vdw
     2.472 3.040
  ... (remaining 16593 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:          0.040
  Check model and map are aligned:         0.020
  Set scattering table:                    0.000
  Process input model:                     3.980
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
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      :  0.004   0.034   2304  Z= 0.266
  Angle     :  0.934   9.620   3152  Z= 0.640
  Chirality :  0.067   0.449    366
  Planarity :  0.004   0.030    385
  Dihedral  : 16.003  59.087    738
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.43 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.36 %
  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 aren not related in a simple way.
  whole: -0.50 (0.52), residues: 290
  helix:  0.67 (0.41), residues: 196
  sheet:  None (None), residues: 0
  loop : -2.51 (0.60), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 219 
 TYR   0.011   0.001   TYR R  99 
 PHE   0.006   0.001   PHE R 286 
 TRP   0.013   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 2302)
  covalent geometry    : angle       0.93489 ( 3148)
  SS BOND              : bond        0.00555 (    2)
  SS BOND              : angle       0.45781 (    4)
  hydrogen bonds       : bond        0.17853 (  144)
  hydrogen bonds       : angle       6.38489 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.083 
Fit side-chains
REVERT: R  255 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8416 (tttm)
  outliers start: 6
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0924
  time to fit residues: 3.1687
Evaluate side-chains
  22 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  128 ILE
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.104289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.090736 restraints weight = 4029.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.16
r_work: 0.3064 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2304  Z= 0.131
  Angle     :  0.537   5.369   3152  Z= 0.282
  Chirality :  0.040   0.121    366
  Planarity :  0.003   0.027    385
  Dihedral  :  6.781  57.631    328
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.33 %
    Favored  : 75.36 %
  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 aren not related in a simple way.
  whole:  0.38 (0.55), residues: 290
  helix:  1.21 (0.40), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.52 (0.65), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.015   0.001   TYR R 274 
 PHE   0.008   0.001   PHE R 117 
 TRP   0.015   0.001   TRP R 317 
 HIS   0.001   0.001   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2302)
  covalent geometry    : angle       0.53648 ( 3148)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.85422 (    4)
  hydrogen bonds       : bond        0.04287 (  144)
  hydrogen bonds       : angle       4.25046 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.088 
Fit side-chains
REVERT: R  258 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7725 (ttmt)
  outliers start: 7
  outliers final: 4
  residues processed: 29
  average time/residue: 0.1011
  time to fit residues: 3.3250
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  186 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 27 optimal weight:    0.1980
   chunk 15 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.086047 restraints weight = 4290.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.10
r_work: 0.3008 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2304  Z= 0.180
  Angle     :  0.574   5.433   3152  Z= 0.302
  Chirality :  0.040   0.120    366
  Planarity :  0.003   0.025    385
  Dihedral  :  5.899  55.567    325
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.70 %
    Favored  : 71.56 %
  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 aren not related in a simple way.
  whole:  0.47 (0.54), residues: 290
  helix:  1.33 (0.40), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.70 (0.65), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.014   0.001   TYR R 283 
 PHE   0.010   0.001   PHE R 100 
 TRP   0.016   0.001   TRP R 317 
 HIS   0.002   0.001   HIS R  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 2302)
  covalent geometry    : angle       0.57215 ( 3148)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.33391 (    4)
  hydrogen bonds       : bond        0.05607 (  144)
  hydrogen bonds       : angle       4.28827 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.088 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 30
  average time/residue: 0.0996
  time to fit residues: 3.3946
Evaluate side-chains
  29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  269 VAL
Chi-restraints excluded: chain R residue  302 TYR
Chi-restraints excluded: chain R residue  326 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.102748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.090599 restraints weight = 4124.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.99
r_work: 0.3085 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2304  Z= 0.112
  Angle     :  0.500   5.483   3152  Z= 0.259
  Chirality :  0.038   0.118    366
  Planarity :  0.003   0.025    385
  Dihedral  :  5.893  55.301    325
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 24.64 %
    Favored  : 70.62 %
  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 aren not related in a simple way.
  whole:  0.66 (0.55), residues: 290
  helix:  1.48 (0.40), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.65 (0.66), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.008   0.001   TYR R 283 
 PHE   0.006   0.001   PHE R 206 
 TRP   0.010   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2302)
  covalent geometry    : angle       0.49896 ( 3148)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.89422 (    4)
  hydrogen bonds       : bond        0.03741 (  144)
  hydrogen bonds       : angle       3.91944 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.085 
Fit side-chains
  outliers start: 10
  outliers final: 3
  residues processed: 30
  average time/residue: 0.1102
  time to fit residues: 3.7279
Evaluate side-chains
  26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  230 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8038

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.103976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.091307 restraints weight = 4036.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.00
r_work: 0.3097 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2304  Z= 0.106
  Angle     :  0.489   5.478   3152  Z= 0.251
  Chirality :  0.038   0.117    366
  Planarity :  0.003   0.023    385
  Dihedral  :  5.187  58.138    324
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.22 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.54), residues: 290
  helix:  1.46 (0.40), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.42 (0.67), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.008   0.001   TYR R 274 
 PHE   0.007   0.001   PHE R 206 
 TRP   0.010   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2302)
  covalent geometry    : angle       0.48835 ( 3148)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       0.95780 (    4)
  hydrogen bonds       : bond        0.03542 (  144)
  hydrogen bonds       : angle       3.82387 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.054 
Fit side-chains
  outliers start: 10
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0964
  time to fit residues: 3.1886
Evaluate side-chains
  23 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   90 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.102836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090334 restraints weight = 4061.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.99
r_work: 0.3080 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2304  Z= 0.117
  Angle     :  0.501   5.651   3152  Z= 0.257
  Chirality :  0.038   0.118    366
  Planarity :  0.003   0.023    385
  Dihedral  :  5.155  57.589    324
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 26.54 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.54), residues: 290
  helix:  1.51 (0.39), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.32 (0.68), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.009   0.001   TYR R 274 
 PHE   0.007   0.001   PHE R 206 
 TRP   0.011   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2302)
  covalent geometry    : angle       0.50004 ( 3148)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.90210 (    4)
  hydrogen bonds       : bond        0.03829 (  144)
  hydrogen bonds       : angle       3.82619 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.081 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 27
  average time/residue: 0.1065
  time to fit residues: 3.2448
Evaluate side-chains
  25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  230 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.089619 restraints weight = 4078.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.16
r_work: 0.3063 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2304  Z= 0.120
  Angle     :  0.517   6.304   3152  Z= 0.264
  Chirality :  0.038   0.119    366
  Planarity :  0.003   0.023    385
  Dihedral  :  5.252  59.312    324
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 27.96 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.53), residues: 290
  helix:  1.60 (0.38), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.23 (0.69), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.009   0.001   TYR R 274 
 PHE   0.007   0.001   PHE R 206 
 TRP   0.010   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2302)
  covalent geometry    : angle       0.51592 ( 3148)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       1.18932 (    4)
  hydrogen bonds       : bond        0.03841 (  144)
  hydrogen bonds       : angle       3.82635 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0919
  time to fit residues: 2.7749
Evaluate side-chains
  24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue  135 THR
Chi-restraints excluded: chain R residue  230 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.103832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.090821 restraints weight = 4018.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.15
r_work: 0.3086 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2304  Z= 0.107
  Angle     :  0.495   6.424   3152  Z= 0.253
  Chirality :  0.038   0.118    366
  Planarity :  0.003   0.023    385
  Dihedral  :  5.211  59.129    324
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 27.96 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.54), residues: 290
  helix:  1.77 (0.38), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.07 (0.71), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.009   0.001   TYR R 274 
 PHE   0.007   0.001   PHE R 206 
 TRP   0.009   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 2302)
  covalent geometry    : angle       0.49408 ( 3148)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       1.06569 (    4)
  hydrogen bonds       : bond        0.03455 (  144)
  hydrogen bonds       : angle       3.75539 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.049 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1141
  time to fit residues: 3.5305
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  230 LYS
Chi-restraints excluded: chain R residue  326 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0770
   chunk 23 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 21 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.108428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.095213 restraints weight = 4023.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.17
r_work: 0.3153 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2304  Z= 0.093
  Angle     :  0.483   7.367   3152  Z= 0.245
  Chirality :  0.037   0.119    366
  Planarity :  0.003   0.024    385
  Dihedral  :  5.072  59.112    324
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 28.91 %
    Favored  : 69.19 %
  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 aren not related in a simple way.
  whole:  1.35 (0.54), residues: 290
  helix:  1.82 (0.39), residues: 215
  sheet:  None (None), residues: 0
  loop : -1.92 (0.74), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.007   0.001   TYR R 274 
 PHE   0.005   0.000   PHE R 117 
 TRP   0.007   0.001   TRP R  98 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 2302)
  covalent geometry    : angle       0.48265 ( 3148)
  SS BOND              : bond        0.00184 (    2)
  SS BOND              : angle       0.80457 (    4)
  hydrogen bonds       : bond        0.02582 (  144)
  hydrogen bonds       : angle       3.60589 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.066 
Fit side-chains
REVERT: R  230 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7349 (tppt)
REVERT: R  232 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7875 (mm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1000
  time to fit residues: 3.3999
Evaluate side-chains
  28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  230 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.106805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.094049 restraints weight = 4129.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.05
r_work: 0.3147 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2304  Z= 0.100
  Angle     :  0.490   7.758   3152  Z= 0.251
  Chirality :  0.037   0.117    366
  Planarity :  0.003   0.020    385
  Dihedral  :  5.095  59.645    324
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 28.44 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.54), residues: 290
  helix:  2.10 (0.39), residues: 207
  sheet:  None (None), residues: 0
  loop : -1.97 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.008   0.001   TYR R 274 
 PHE   0.006   0.001   PHE R 206 
 TRP   0.009   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 2302)
  covalent geometry    : angle       0.48987 ( 3148)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.83869 (    4)
  hydrogen bonds       : bond        0.02990 (  144)
  hydrogen bonds       : angle       3.67461 (  432)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.100 
Fit side-chains
REVERT: R  230 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7419 (tppt)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.1028
  time to fit residues: 2.9787
Evaluate side-chains
  26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 VAL
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  230 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.106481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.093744 restraints weight = 4099.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.10
r_work: 0.3138 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2304  Z= 0.101
  Angle     :  0.505   7.429   3152  Z= 0.254
  Chirality :  0.037   0.117    366
  Planarity :  0.003   0.020    385
  Dihedral  :  5.100  59.759    324
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 28.91 %
    Favored  : 69.67 %
  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 aren not related in a simple way.
  whole:  1.60 (0.54), residues: 290
  helix:  2.17 (0.39), residues: 207
  sheet:  None (None), residues: 0
  loop : -1.96 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 219 
 TYR   0.008   0.001   TYR R 274 
 PHE   0.006   0.001   PHE R 206 
 TRP   0.009   0.001   TRP R 317 
 HIS   0.001   0.000   HIS R  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 2302)
  covalent geometry    : angle       0.50478 ( 3148)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       0.85121 (    4)
  hydrogen bonds       : bond        0.03087 (  144)
  hydrogen bonds       : angle       3.66308 (  432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 742.12 seconds
wall clock time: 13 minutes 17.13 seconds (797.13 seconds total)