Starting phenix.real_space_refine
on Tue Mar  3 12:03:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7knu_22963/03_2026/7knu_22963.map"
  }
  resolution = 3.49
  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=  -0.001 sd=   0.033
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      31      5.16       5
     C    2504      2.51       5
     N     631      2.21       5
     O     643      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3809
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 931
          Classifications: {'peptide': 115}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108}
    Chain: "P"
      Number of atoms: 82
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 82
          Classifications: {'peptide': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 9}
    Chain: "R"
      Number of atoms: 2796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2796
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 9, 'TRANS': 331}
          Chain breaks: 4
  Time building chain proxies: 1.00, per 1000 atoms: 0.26
  Number of scatterers: 3809
  At special positions: 0
  Unit cell: (63.08, 105.41, 82.17, 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      31     16.00
     O     643      8.00
     N     631      7.00
     C    2504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  40 " - pdb=" SG  CYS E  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  57 " - pdb=" SG  CYS E 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  65 " - pdb=" SG  CYS R 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  88 " - pdb=" SG  CYS R 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 212 " - pdb=" SG  CYS R 282 " distance=2.03

  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: 0.31
  Conformation dependent library (CDL) restraints added in 157.1 milliseconds
  

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  890

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      68.3% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'E' and resid 29 through 35
      removed outlier: 3.547A  pdb=" N   LEU E  35 " --> pdb=" O   ASN E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 50
      removed outlier: 3.676A  pdb=" N   GLN E  45 " --> pdb=" O   LEU E  41 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL E  46 " --> pdb=" O   THR E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 80
      removed outlier: 5.458A  pdb=" N   ARG E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   SER E  65 " --> pdb=" O   ARG E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 101
      removed outlier: 3.759A  pdb=" N   ARG E  91 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   PHE E  92 " --> pdb=" O   GLU E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 143
      removed outlier: 4.031A  pdb=" N   PHE E 122 " --> pdb=" O   ILE E 118 " (cutoff:3.500A)
      Proline residue:  E 126  - end of helix
      removed outlier: 3.911A  pdb=" N   LEU E 131 " --> pdb=" O   ILE E 127 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ALA E 135 " --> pdb=" O   LEU E 131 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG E 143 " --> pdb=" O   TRP E 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 34 through 54
      removed outlier: 4.082A  pdb=" N   ALA R  44 " --> pdb=" O   LYS R  40 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR R  49 " --> pdb=" O   GLN R  45 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN R  50 " --> pdb=" O   TYR R  46 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS R  51 " --> pdb=" O   GLU R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 167
      removed outlier: 3.719A  pdb=" N   PHE R 142 " --> pdb=" O   ALA R 138 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE R 147 " --> pdb=" O   TYR R 143 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ILE R 153 " --> pdb=" O   HIS R 149 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA R 154 " --> pdb=" O   GLY R 150 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER R 159 " --> pdb=" O   SER R 155 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE R 162 " --> pdb=" O   ILE R 158 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE R 163 " --> pdb=" O   SER R 159 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R 166 " --> pdb=" O   ILE R 162 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LYS R 167 " --> pdb=" O   PHE R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 192
      removed outlier: 4.146A  pdb=" N   ASN R 179 " --> pdb=" O   THR R 175 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE R 182 " --> pdb=" O   LYS R 178 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE R 192 " --> pdb=" O   SER R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 208
    Processing helix  chain 'R' and resid 209 through 242
      removed outlier: 3.678A  pdb=" N   LYS R 213 " --> pdb=" O   PRO R 209 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY R 224 " --> pdb=" O   LEU R 220 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   MET R 230 " --> pdb=" O   ASN R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 263 through 278
      removed outlier: 3.734A  pdb=" N   SER R 275 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU R 276 " --> pdb=" O   ILE R 272 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR R 277 " --> pdb=" O   ALA R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 284
      removed outlier: 3.535A  pdb=" N   TRP R 283 " --> pdb=" O   ASP R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 291 through 319
      Proline residue:  R 297  - end of helix
      removed outlier: 3.505A  pdb=" N   LEU R 306 " --> pdb=" O   LEU R 302 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN R 311 " --> pdb=" O   PHE R 307 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE R 317 " --> pdb=" O   VAL R 313 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR R 318 " --> pdb=" O   ARG R 314 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LYS R 319 " --> pdb=" O   VAL R 315 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 331 through 351
      removed outlier: 3.668A  pdb=" N   VAL R 335 " --> pdb=" O   TYR R 331 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA R 337 " --> pdb=" O   LYS R 333 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU R 341 " --> pdb=" O   ALA R 337 " (cutoff:3.500A)
      Proline residue:  R 343  - end of helix
      removed outlier: 5.650A  pdb=" N   GLU R 348 " --> pdb=" O   LEU R 344 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   PHE R 349 " --> pdb=" O   LEU R 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 375
      removed outlier: 3.596A  pdb=" N   HIS R 374 " --> pdb=" O   HIS R 370 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 375 through 385
    Processing helix  chain 'R' and resid 388 through 402
    Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 87
      removed outlier: 3.507A  pdb=" N   GLN R  86 " --> pdb=" O   VAL R 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 113 through 114

    199 hydrogen bonds defined for protein.
    591 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: 0.48

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1162
        1.34 -     1.46: 1033
        1.46 -     1.58: 1681
        1.58 -     1.70: 0
        1.70 -     1.81: 42
  Bond restraints: 3918
  Sorted by residual:
  bond pdb=" C   TYR E 120 "
       pdb=" N   PRO E 121 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.13e+00
  bond pdb=" CA  MET R 253 "
       pdb=" C   MET R 253 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 1.29e-02 6.01e+03 1.85e+00
  bond pdb=" N   LEU R 252 "
       pdb=" CA  LEU R 252 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.015 1.29e-02 6.01e+03 1.42e+00
  bond pdb=" CA  TRP R 254 "
       pdb=" C   TRP R 254 "
    ideal  model  delta    sigma   weight residual
    1.523  1.509  0.015 1.30e-02 5.92e+03 1.28e+00
  bond pdb=" N   ARG R 173 "
       pdb=" CA  ARG R 173 "
    ideal  model  delta    sigma   weight residual
    1.459  1.445  0.014 1.21e-02 6.83e+03 1.27e+00
  ... (remaining 3913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 5149
        1.45 -     2.90: 145
        2.90 -     4.34: 22
        4.34 -     5.79: 15
        5.79 -     7.24: 3
  Bond angle restraints: 5334
  Sorted by residual:
  angle pdb=" N   ALA R 247 "
        pdb=" CA  ALA R 247 "
        pdb=" C   ALA R 247 "
      ideal   model   delta    sigma   weight residual
     110.10  103.85    6.25 1.49e+00 4.50e-01 1.76e+01
  angle pdb=" N   MET R 253 "
        pdb=" CA  MET R 253 "
        pdb=" C   MET R 253 "
      ideal   model   delta    sigma   weight residual
     111.36  107.96    3.40 1.09e+00 8.42e-01 9.72e+00
  angle pdb=" N   LYS R 249 "
        pdb=" CA  LYS R 249 "
        pdb=" C   LYS R 249 "
      ideal   model   delta    sigma   weight residual
     108.90  113.91   -5.01 1.63e+00 3.76e-01 9.44e+00
  angle pdb=" N   LEU R 252 "
        pdb=" CA  LEU R 252 "
        pdb=" C   LEU R 252 "
      ideal   model   delta    sigma   weight residual
     110.80  116.79   -5.99 2.13e+00 2.20e-01 7.91e+00
  angle pdb=" C   GLU R 248 "
        pdb=" N   LYS R 249 "
        pdb=" CA  LYS R 249 "
      ideal   model   delta    sigma   weight residual
     122.99  119.22    3.77 1.41e+00 5.03e-01 7.16e+00
  ... (remaining 5329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 2015
       17.76 -    35.52: 205
       35.52 -    53.28: 36
       53.28 -    71.04: 5
       71.04 -    88.80: 3
  Dihedral angle restraints: 2264
    sinusoidal: 891
      harmonic: 1373
  Sorted by residual:
  dihedral pdb=" CB  CYS R 212 "
           pdb=" SG  CYS R 212 "
           pdb=" SG  CYS R 282 "
           pdb=" CB  CYS R 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.74   49.26     1      1.00e+01 1.00e-02 3.33e+01
  dihedral pdb=" CB  CYS E  40 "
           pdb=" SG  CYS E  40 "
           pdb=" SG  CYS E  72 "
           pdb=" CB  CYS E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.64   40.36     1      1.00e+01 1.00e-02 2.29e+01
  dihedral pdb=" CB  CYS E  57 "
           pdb=" SG  CYS E  57 "
           pdb=" SG  CYS E 104 "
           pdb=" CB  CYS E 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.81   35.81     1      1.00e+01 1.00e-02 1.81e+01
  ... (remaining 2261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 563
       0.077 -    0.153: 30
       0.153 -    0.230: 4
       0.230 -    0.307: 1
       0.307 -    0.383: 1
  Chirality restraints: 599
  Sorted by residual:
  chirality pdb=" CA  PHE R 246 "
            pdb=" N   PHE R 246 "
            pdb=" C   PHE R 246 "
            pdb=" CB  PHE R 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.68e+00
  chirality pdb=" CA  LEU R 252 "
            pdb=" N   LEU R 252 "
            pdb=" C   LEU R 252 "
            pdb=" CB  LEU R 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  GLU R 248 "
            pdb=" N   GLU R 248 "
            pdb=" C   GLU R 248 "
            pdb=" CB  GLU R 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.32e-01
  ... (remaining 596 not shown)

  Planarity restraints: 653
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R  96 "    0.073 5.00e-02 4.00e+02   1.10e-01 1.95e+01
        pdb=" N   PRO R  97 "   -0.191 5.00e-02 4.00e+02
        pdb=" CA  PRO R  97 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO R  97 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 296 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.62e+00
        pdb=" N   PRO R 297 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO R 297 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 297 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  96 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   ASP R  96 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASP R  96 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   PRO R  97 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 650 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 72
        2.69 -     3.24: 4048
        3.24 -     3.80: 6093
        3.80 -     4.35: 8134
        4.35 -     4.90: 12421
  Nonbonded interactions: 30768
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 285 "
            pdb=" OD1 ASP R 287 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   GLY E  33 "
            pdb=" NH1 ARG E  37 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" O   SER R 170 "
            pdb=" OG  SER R 170 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER R 155 "
            pdb=" OG  SER R 381 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OE2 GLU E  29 "
            pdb=" ND2 ASN E  31 "
     model   vdw
     2.352 3.120
  ... (remaining 30763 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=0.00 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:             0.940
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.530
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
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   0.038   3924  Z= 0.154
  Angle     :  0.643   7.242   5346  Z= 0.371
  Chirality :  0.045   0.383    599
  Planarity :  0.005   0.110    653
  Dihedral  : 14.107  88.802   1356
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.59 (0.39), residues: 453
  helix: -0.62 (0.30), residues: 298
  sheet: -1.73 (1.17), residues: 12
  loop : -1.67 (0.50), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  37 
 TYR   0.005   0.001   TYR R 365 
 PHE   0.007   0.001   PHE R 384 
 TRP   0.009   0.001   TRP R  69 
 HIS   0.003   0.001   HIS R 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3918)
  covalent geometry    : angle       0.64295 ( 5334)
  SS BOND              : bond        0.00124 (    6)
  SS BOND              : angle       0.54485 (   12)
  hydrogen bonds       : bond        0.28911 (  199)
  hydrogen bonds       : angle       8.60424 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: E   76 MET cc_start: 0.8313 (mpp) cc_final: 0.7857 (mpp)
REVERT: R  100 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8254 (mmtm)
REVERT: R  248 GLU cc_start: 0.8119 (tp30) cc_final: 0.7904 (tm-30)
REVERT: R  264 LEU cc_start: 0.8941 (tp) cc_final: 0.8640 (tp)
REVERT: R  369 MET cc_start: 0.8294 (mmm) cc_final: 0.7986 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0838
  time to fit residues: 7.3470
Evaluate side-chains
  44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
R 219 HIS
R 250 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.093100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.075447 restraints weight = 15655.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 4.74
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3924  Z= 0.160
  Angle     :  0.624   5.770   5346  Z= 0.327
  Chirality :  0.041   0.132    599
  Planarity :  0.005   0.081    653
  Dihedral  :  4.551  15.470    503
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.43 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.18 (0.39), residues: 453
  helix: -0.19 (0.30), residues: 305
  sheet: -1.38 (1.22), residues: 12
  loop : -1.88 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  37 
 TYR   0.009   0.001   TYR E  66 
 PHE   0.013   0.001   PHE E  44 
 TRP   0.012   0.001   TRP R 254 
 HIS   0.009   0.001   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3918)
  covalent geometry    : angle       0.62312 ( 5334)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.87725 (   12)
  hydrogen bonds       : bond        0.05621 (  199)
  hydrogen bonds       : angle       5.14472 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   85 MET cc_start: 0.9012 (tpp) cc_final: 0.8645 (tpp)
REVERT: R  248 GLU cc_start: 0.8125 (tp30) cc_final: 0.7759 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0674
  time to fit residues: 4.8728
Evaluate side-chains
  51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   43 THR
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** R 305 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 = 0.3872 r_free = 0.3872 target = 0.091614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.074266 restraints weight = 15491.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 4.66
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3924  Z= 0.161
  Angle     :  0.597   5.959   5346  Z= 0.309
  Chirality :  0.041   0.227    599
  Planarity :  0.004   0.068    653
  Dihedral  :  4.600  15.871    503
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.81 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 (0.40), residues: 453
  helix: -0.01 (0.31), residues: 304
  sheet: -0.96 (1.23), residues: 12
  loop : -1.90 (0.52), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 173 
 TYR   0.007   0.001   TYR R 236 
 PHE   0.011   0.001   PHE R 349 
 TRP   0.028   0.001   TRP R 254 
 HIS   0.008   0.001   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3918)
  covalent geometry    : angle       0.59657 ( 5334)
  SS BOND              : bond        0.00229 (    6)
  SS BOND              : angle       0.74487 (   12)
  hydrogen bonds       : bond        0.04600 (  199)
  hydrogen bonds       : angle       4.66512 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   85 MET cc_start: 0.8789 (tpp) cc_final: 0.8588 (tpp)
REVERT: R  248 GLU cc_start: 0.8237 (tp30) cc_final: 0.7797 (tm-30)
REVERT: R  262 PHE cc_start: 0.8728 (t80) cc_final: 0.8513 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 58
  average time/residue: 0.0606
  time to fit residues: 4.3685
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   43 THR
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0070
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.9202

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.092888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.075637 restraints weight = 15180.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 4.65
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3924  Z= 0.117
  Angle     :  0.565   6.051   5346  Z= 0.286
  Chirality :  0.039   0.210    599
  Planarity :  0.004   0.058    653
  Dihedral  :  4.478  14.138    503
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.18 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.69 (0.40), residues: 453
  helix:  0.26 (0.31), residues: 295
  sheet: -0.15 (1.40), residues: 12
  loop : -1.87 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 173 
 TYR   0.007   0.001   TYR R 227 
 PHE   0.005   0.001   PHE R 184 
 TRP   0.011   0.001   TRP R 254 
 HIS   0.007   0.001   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3918)
  covalent geometry    : angle       0.56475 ( 5334)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.67583 (   12)
  hydrogen bonds       : bond        0.04033 (  199)
  hydrogen bonds       : angle       4.39025 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  248 GLU cc_start: 0.8289 (tp30) cc_final: 0.7841 (tm-30)
REVERT: R  262 PHE cc_start: 0.8725 (t80) cc_final: 0.8460 (t80)
  outliers start: 6
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0556
  time to fit residues: 4.3515
Evaluate side-chains
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** R 305 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 = 0.3884 r_free = 0.3884 target = 0.090443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.072880 restraints weight = 15543.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 4.55
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   3924  Z= 0.242
  Angle     :  0.674   6.013   5346  Z= 0.343
  Chirality :  0.042   0.178    599
  Planarity :  0.004   0.055    653
  Dihedral  :  4.716  13.967    503
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.63 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.81 (0.40), residues: 453
  helix:  0.11 (0.31), residues: 301
  sheet: -0.01 (1.47), residues: 12
  loop : -1.87 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 119 
 TYR   0.012   0.002   TYR R 236 
 PHE   0.016   0.002   PHE R 349 
 TRP   0.012   0.001   TRP R 254 
 HIS   0.008   0.002   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 3918)
  covalent geometry    : angle       0.67292 ( 5334)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       1.18145 (   12)
  hydrogen bonds       : bond        0.04324 (  199)
  hydrogen bonds       : angle       4.54862 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8650 (mp0) cc_final: 0.8332 (mp0)
REVERT: R   85 MET cc_start: 0.8808 (tpp) cc_final: 0.8548 (tpp)
REVERT: R  147 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8443 (tp)
REVERT: R  223 MET cc_start: 0.8450 (mtt) cc_final: 0.8158 (mtm)
REVERT: R  248 GLU cc_start: 0.8373 (tp30) cc_final: 0.7996 (tm-30)
REVERT: R  262 PHE cc_start: 0.8673 (t80) cc_final: 0.8379 (t80)
REVERT: R  378 LEU cc_start: 0.8793 (mt) cc_final: 0.8128 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0592
  time to fit residues: 4.5421
Evaluate side-chains
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   43 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0570
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7898

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

Flipped N/Q/H residues before XYZ refinement:
** R 305 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 = 0.3931 r_free = 0.3931 target = 0.093288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.075788 restraints weight = 15381.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 4.61
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3924  Z= 0.118
  Angle     :  0.592   6.161   5346  Z= 0.296
  Chirality :  0.040   0.186    599
  Planarity :  0.004   0.050    653
  Dihedral  :  4.574  15.713    503
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.07 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.40), residues: 453
  helix:  0.35 (0.31), residues: 295
  sheet:  0.20 (1.48), residues: 12
  loop : -1.91 (0.50), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 173 
 TYR   0.008   0.001   TYR R 227 
 PHE   0.006   0.001   PHE R 349 
 TRP   0.009   0.001   TRP R 229 
 HIS   0.007   0.001   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3918)
  covalent geometry    : angle       0.59130 ( 5334)
  SS BOND              : bond        0.00200 (    6)
  SS BOND              : angle       0.86821 (   12)
  hydrogen bonds       : bond        0.03793 (  199)
  hydrogen bonds       : angle       4.27301 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8674 (mp0) cc_final: 0.8322 (mp0)
REVERT: R   85 MET cc_start: 0.8693 (tpp) cc_final: 0.8400 (tpp)
REVERT: R  248 GLU cc_start: 0.8354 (tp30) cc_final: 0.7957 (tm-30)
REVERT: R  262 PHE cc_start: 0.8691 (t80) cc_final: 0.8408 (t80)
REVERT: R  349 PHE cc_start: 0.8700 (m-80) cc_final: 0.8491 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0521
  time to fit residues: 4.2761
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   chunk 7 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3682

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

Flipped N/Q/H residues before XYZ refinement:
** R 305 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 = 0.3884 r_free = 0.3884 target = 0.092142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.074790 restraints weight = 15755.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 4.81
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3924  Z= 0.133
  Angle     :  0.618   7.913   5346  Z= 0.310
  Chirality :  0.041   0.265    599
  Planarity :  0.004   0.049    653
  Dihedral  :  4.500  13.177    503
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.04 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.54 (0.41), residues: 453
  helix:  0.33 (0.31), residues: 301
  sheet:  0.37 (1.53), residues: 12
  loop : -1.84 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 173 
 TYR   0.006   0.001   TYR R 227 
 PHE   0.006   0.001   PHE R 349 
 TRP   0.010   0.001   TRP R 229 
 HIS   0.008   0.001   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3918)
  covalent geometry    : angle       0.61800 ( 5334)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       0.74424 (   12)
  hydrogen bonds       : bond        0.03730 (  199)
  hydrogen bonds       : angle       4.30310 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8714 (mp0) cc_final: 0.8358 (mp0)
REVERT: R   85 MET cc_start: 0.8698 (tpp) cc_final: 0.8461 (tpp)
REVERT: R  248 GLU cc_start: 0.8371 (tp30) cc_final: 0.7947 (tm-30)
REVERT: R  262 PHE cc_start: 0.8766 (t80) cc_final: 0.8528 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 61
  average time/residue: 0.0693
  time to fit residues: 5.3988
Evaluate side-chains
  58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  350 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 305 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 = 0.3900 r_free = 0.3900 target = 0.093122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.075945 restraints weight = 15417.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 4.82
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3924  Z= 0.121
  Angle     :  0.618   6.926   5346  Z= 0.305
  Chirality :  0.040   0.207    599
  Planarity :  0.004   0.047    653
  Dihedral  :  4.469  15.736    503
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.31 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.49 (0.40), residues: 453
  helix:  0.41 (0.31), residues: 293
  sheet:  0.54 (1.56), residues: 12
  loop : -1.84 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 173 
 TYR   0.010   0.001   TYR E 100 
 PHE   0.005   0.001   PHE R 184 
 TRP   0.010   0.001   TRP R 229 
 HIS   0.004   0.001   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3918)
  covalent geometry    : angle       0.61799 ( 5334)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       0.64070 (   12)
  hydrogen bonds       : bond        0.03620 (  199)
  hydrogen bonds       : angle       4.28340 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8718 (mp0) cc_final: 0.8355 (mp0)
REVERT: R   85 MET cc_start: 0.8607 (tpp) cc_final: 0.8351 (tpp)
REVERT: R  223 MET cc_start: 0.8441 (mtt) cc_final: 0.8045 (mtm)
REVERT: R  228 PHE cc_start: 0.9139 (m-10) cc_final: 0.8929 (m-10)
REVERT: R  248 GLU cc_start: 0.8364 (tp30) cc_final: 0.7863 (tm-30)
REVERT: R  262 PHE cc_start: 0.8808 (t80) cc_final: 0.8561 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0613
  time to fit residues: 5.3145
Evaluate side-chains
  60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0870
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.4162

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 305 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 = 0.3894 r_free = 0.3894 target = 0.092463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.075154 restraints weight = 15358.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 4.79
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3924  Z= 0.138
  Angle     :  0.669  15.875   5346  Z= 0.324
  Chirality :  0.044   0.445    599
  Planarity :  0.004   0.047    653
  Dihedral  :  4.495  14.005    503
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 19.52 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.49 (0.40), residues: 453
  helix:  0.36 (0.31), residues: 299
  sheet:  0.55 (1.60), residues: 12
  loop : -1.78 (0.52), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 173 
 TYR   0.007   0.001   TYR R 227 
 PHE   0.007   0.001   PHE R 349 
 TRP   0.011   0.001   TRP R  72 
 HIS   0.005   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3918)
  covalent geometry    : angle       0.66923 ( 5334)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       0.74883 (   12)
  hydrogen bonds       : bond        0.03657 (  199)
  hydrogen bonds       : angle       4.23156 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8738 (mp0) cc_final: 0.8375 (mp0)
REVERT: R   85 MET cc_start: 0.8516 (tpp) cc_final: 0.8272 (tpp)
REVERT: R  223 MET cc_start: 0.8435 (mtt) cc_final: 0.8087 (mtm)
REVERT: R  248 GLU cc_start: 0.8404 (tp30) cc_final: 0.7886 (tm-30)
REVERT: R  262 PHE cc_start: 0.8824 (t80) cc_final: 0.8556 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 58
  average time/residue: 0.0634
  time to fit residues: 4.7947
Evaluate side-chains
  59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 305 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 = 0.3848 r_free = 0.3848 target = 0.089752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.072239 restraints weight = 15793.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 4.76
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3924  Z= 0.226
  Angle     :  0.758  14.962   5346  Z= 0.370
  Chirality :  0.048   0.472    599
  Planarity :  0.005   0.049    653
  Dihedral  :  4.769  20.305    503
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 19.52 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.71 (0.40), residues: 453
  helix:  0.16 (0.31), residues: 299
  sheet:  0.09 (1.42), residues: 12
  loop : -1.76 (0.53), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 119 
 TYR   0.012   0.002   TYR R 236 
 PHE   0.016   0.001   PHE R 349 
 TRP   0.010   0.001   TRP R  72 
 HIS   0.006   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 3918)
  covalent geometry    : angle       0.75705 ( 5334)
  SS BOND              : bond        0.00524 (    6)
  SS BOND              : angle       1.05376 (   12)
  hydrogen bonds       : bond        0.03987 (  199)
  hydrogen bonds       : angle       4.41404 (  591)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 GLU cc_start: 0.8734 (mp0) cc_final: 0.8366 (mp0)
REVERT: R   90 ASP cc_start: 0.9298 (p0) cc_final: 0.8950 (m-30)
REVERT: R  223 MET cc_start: 0.8483 (mtt) cc_final: 0.8130 (mtm)
REVERT: R  248 GLU cc_start: 0.8451 (tp30) cc_final: 0.7965 (tm-30)
REVERT: R  262 PHE cc_start: 0.8772 (t80) cc_final: 0.8519 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0601
  time to fit residues: 4.0921
Evaluate side-chains
  53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  189 VAL
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain R residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0020
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0270
   chunk 28 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7848

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

Flipped N/Q/H residues before XYZ refinement:
R  50 GLN
** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.092853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.075286 restraints weight = 15655.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 4.81
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3924  Z= 0.127
  Angle     :  0.722  15.224   5346  Z= 0.342
  Chirality :  0.044   0.444    599
  Planarity :  0.004   0.053    653
  Dihedral  :  4.682  19.943    503
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 20.72 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -0.54 (0.41), residues: 453
  helix:  0.22 (0.31), residues: 301
  sheet:  1.06 (1.62), residues: 12
  loop : -1.63 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  99 
 TYR   0.040   0.001   TYR R 143 
 PHE   0.006   0.001   PHE R 349 
 TRP   0.014   0.001   TRP R  72 
 HIS   0.003   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3918)
  covalent geometry    : angle       0.72141 ( 5334)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.91611 (   12)
  hydrogen bonds       : bond        0.03608 (  199)
  hydrogen bonds       : angle       4.25894 (  591)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 907.11 seconds
wall clock time: 16 minutes 15.06 seconds (975.06 seconds total)