Starting phenix.real_space_refine
on Tue Mar  3 10:50:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2026/8ggw_40023.map"
  }
  resolution = 3.6
  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=   0.020
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    1379      2.51       5
     N     335      2.21       5
     O     353      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 2079
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2064
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 245
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.73, per 1000 atoms: 0.35
  Number of scatterers: 2079
  At special positions: 0
  Unit cell: (54.6651, 83.2992, 62.4744, 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     353      8.00
     N     335      7.00
     C    1379      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - 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: 0.20
  Conformation dependent library (CDL) restraints added in 96.4 milliseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 0 sheets defined
      85.8% 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 32 through 61
      removed outlier: 3.627A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.940A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
      removed outlier: 3.643A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   HIS R  93 " --> pdb=" O   PHE R  89 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE R  94 " --> pdb=" O   GLY R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 137
      removed outlier: 3.847A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.790A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.619A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 198 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.883A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS R 235 " --> pdb=" O   GLN R 231 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      Proline residue:  R 288  - end of helix
      removed outlier: 3.918A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.874A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340

    161 hydrogen bonds defined for protein.
    483 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: 0.29

  Time building geometry restraints manager: 0.25 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: 638
        1.34 -     1.46: 583
        1.46 -     1.58: 897
        1.58 -     1.70: 0
        1.70 -     1.82: 17
  Bond restraints: 2135
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.18e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.61e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.25e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.85e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.323  0.030 2.00e-02 2.50e+03 2.29e+00
  ... (remaining 2130 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 2771
        1.18 -     2.35: 128
        2.35 -     3.53: 22
        3.53 -     4.71: 7
        4.71 -     5.88: 6
  Bond angle restraints: 2934
  Sorted by residual:
  angle pdb=" C   GLU R 180 "
        pdb=" N   ALA R 181 "
        pdb=" CA  ALA R 181 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.48e+00
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     121.58  116.00    5.58 1.95e+00 2.63e-01 8.20e+00
  angle pdb=" N   ILE R 135 "
        pdb=" CA  ILE R 135 "
        pdb=" C   ILE R 135 "
      ideal   model   delta    sigma   weight residual
     111.00  113.67   -2.67 1.09e+00 8.42e-01 6.01e+00
  angle pdb=" C   ILE R 135 "
        pdb=" CA  ILE R 135 "
        pdb=" CB  ILE R 135 "
      ideal   model   delta    sigma   weight residual
     112.24  109.57    2.67 1.34e+00 5.57e-01 3.98e+00
  angle pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
        pdb=" CB  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     110.41  113.75   -3.34 1.68e+00 3.54e-01 3.96e+00
  ... (remaining 2929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1094
       16.95 -    33.91: 103
       33.91 -    50.86: 15
       50.86 -    67.82: 0
       67.82 -    84.77: 1
  Dihedral angle restraints: 1213
    sinusoidal: 385
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.77  -84.77     1      1.00e+01 1.00e-02 8.73e+01
  dihedral pdb=" CA  CYS R 190 "
           pdb=" C   CYS R 190 "
           pdb=" N   CYS R 191 "
           pdb=" CA  CYS R 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.14  -17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 227
       0.033 -    0.066: 90
       0.066 -    0.098: 31
       0.098 -    0.131: 5
       0.131 -    0.164: 1
  Chirality restraints: 354
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.73e-01
  chirality pdb=" CA  ILE R 303 "
            pdb=" N   ILE R 303 "
            pdb=" C   ILE R 303 "
            pdb=" CB  ILE R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.04e-01
  ... (remaining 351 not shown)

  Planarity restraints: 361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.024 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO R 330 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 173 "   -0.011 2.00e-02 2.50e+03   8.68e-03 1.88e+00
        pdb=" CG  TRP R 173 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 173 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 173 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 173 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 173 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 173 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 173 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 173 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 173 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO R 168 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 358 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 424
        2.77 -     3.30: 2103
        3.30 -     3.84: 3391
        3.84 -     4.37: 3303
        4.37 -     4.90: 6123
  Nonbonded interactions: 15344
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR R 118 "
            pdb=" OG  SER R 161 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" O   VAL R 292 "
            pdb=" ND1 HIS R 296 "
     model   vdw
     2.581 3.120
  ... (remaining 15339 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.490
  Find NCS groups from input model:        0.010
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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   0.054   2137  Z= 0.188
  Angle     :  0.623   5.882   2938  Z= 0.354
  Chirality :  0.040   0.164    354
  Planarity :  0.004   0.037    361
  Dihedral  : 12.729  44.728    669
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.50), residues: 277
  helix:  2.43 (0.35), residues: 206
  sheet:  None (None), residues: 0
  loop : -1.87 (0.60), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.014   0.001   TYR R 185 
 PHE   0.009   0.001   PHE R 290 
 TRP   0.023   0.002   TRP R 173 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 2135)
  covalent geometry    : angle       0.62146 ( 2934)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       1.40087 (    4)
  hydrogen bonds       : bond        0.17170 (  161)
  hydrogen bonds       : angle       5.31519 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0609
  time to fit residues: 2.8921
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.152586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135364 restraints weight = 3273.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140185 restraints weight = 1625.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141714 restraints weight = 782.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142173 restraints weight = 625.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.143591 restraints weight = 563.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2137  Z= 0.141
  Angle     :  0.538   4.946   2938  Z= 0.300
  Chirality :  0.041   0.136    354
  Planarity :  0.004   0.032    361
  Dihedral  :  5.152  18.625    311
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.83 %
    Favored  : 84.04 %
  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 are not related in a simple way.
  whole:  2.15 (0.51), residues: 277
  helix:  2.33 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.94 (0.68), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.013   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R  61 
 TRP   0.020   0.001   TRP R 173 
 HIS   0.001   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2135)
  covalent geometry    : angle       0.53622 ( 2934)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       1.38752 (    4)
  hydrogen bonds       : bond        0.05952 (  161)
  hydrogen bonds       : angle       4.21403 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.076 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.8077 (mm) cc_final: 0.7727 (tt)
REVERT: R  173 TRP cc_start: 0.7144 (m-10) cc_final: 0.6537 (m-90)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0610
  time to fit residues: 2.5533
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0170
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.150665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133268 restraints weight = 3379.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137702 restraints weight = 1689.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.139434 restraints weight = 880.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.140051 restraints weight = 682.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141572 restraints weight = 582.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   2137  Z= 0.147
  Angle     :  0.541   4.855   2938  Z= 0.299
  Chirality :  0.041   0.130    354
  Planarity :  0.004   0.031    361
  Dihedral  :  4.873  18.520    311
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.43 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.51), residues: 277
  helix:  2.27 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.55 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.012   0.001   TYR R 185 
 PHE   0.007   0.001   PHE R  61 
 TRP   0.015   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 2135)
  covalent geometry    : angle       0.53790 ( 2934)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       1.55991 (    4)
  hydrogen bonds       : bond        0.05839 (  161)
  hydrogen bonds       : angle       4.13193 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.045 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6882 (ppp) cc_final: 0.6444 (ptm)
REVERT: R  173 TRP cc_start: 0.7396 (m-10) cc_final: 0.7029 (m-90)
REVERT: R  316 TYR cc_start: 0.7176 (m-10) cc_final: 0.6963 (m-10)
  outliers start: 6
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0529
  time to fit residues: 2.2832
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0040
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.153047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135744 restraints weight = 3309.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139898 restraints weight = 1657.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.142184 restraints weight = 896.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.142911 restraints weight = 658.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.144139 restraints weight = 547.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2137  Z= 0.137
  Angle     :  0.521   5.452   2938  Z= 0.288
  Chirality :  0.040   0.130    354
  Planarity :  0.003   0.029    361
  Dihedral  :  4.700  18.177    311
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.62 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.51), residues: 277
  helix:  2.36 (0.35), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.54 (0.79), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R 217 
 TRP   0.011   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2135)
  covalent geometry    : angle       0.51853 ( 2934)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       1.55977 (    4)
  hydrogen bonds       : bond        0.05531 (  161)
  hydrogen bonds       : angle       4.00937 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.094 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7450 (tt)
REVERT: R  171 MET cc_start: 0.6954 (ppp) cc_final: 0.6717 (ptm)
  outliers start: 7
  outliers final: 5
  residues processed: 34
  average time/residue: 0.0496
  time to fit residues: 2.0439
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.151191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.133847 restraints weight = 3310.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137973 restraints weight = 1704.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140280 restraints weight = 924.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.140867 restraints weight = 672.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.142778 restraints weight = 573.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.150
  Angle     :  0.548   5.912   2938  Z= 0.300
  Chirality :  0.041   0.127    354
  Planarity :  0.003   0.028    361
  Dihedral  :  4.796  18.551    311
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.68 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.51), residues: 277
  helix:  2.44 (0.35), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.73 (0.73), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R  61 
 TRP   0.024   0.002   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2135)
  covalent geometry    : angle       0.54550 ( 2934)
  SS BOND              : bond        0.00466 (    2)
  SS BOND              : angle       1.64241 (    4)
  hydrogen bonds       : bond        0.05858 (  161)
  hydrogen bonds       : angle       4.04157 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.049 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7395 (tt)
REVERT: R  171 MET cc_start: 0.7066 (ppp) cc_final: 0.6041 (ppp)
REVERT: R  173 TRP cc_start: 0.7887 (m-10) cc_final: 0.6670 (m-90)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.0455
  time to fit residues: 1.8981
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.145715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128738 restraints weight = 3336.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131874 restraints weight = 1758.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134550 restraints weight = 1025.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.135021 restraints weight = 727.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.136813 restraints weight = 635.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2137  Z= 0.179
  Angle     :  0.585   6.296   2938  Z= 0.323
  Chirality :  0.042   0.128    354
  Planarity :  0.004   0.030    361
  Dihedral  :  4.940  19.937    311
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 20.21 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.51), residues: 277
  helix:  2.14 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -1.60 (0.77), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.010   0.001   TYR R 185 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.017   0.002   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 2135)
  covalent geometry    : angle       0.58065 ( 2934)
  SS BOND              : bond        0.00550 (    2)
  SS BOND              : angle       1.91765 (    4)
  hydrogen bonds       : bond        0.06540 (  161)
  hydrogen bonds       : angle       4.20570 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.070 
Fit side-chains
REVERT: R  173 TRP cc_start: 0.8037 (m-10) cc_final: 0.7266 (m-90)
  outliers start: 9
  outliers final: 8
  residues processed: 37
  average time/residue: 0.0472
  time to fit residues: 2.1028
Evaluate side-chains
  38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    0.0670
   chunk 14 optimal weight:    0.0570
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4036

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.154275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137921 restraints weight = 3245.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141610 restraints weight = 1734.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.143251 restraints weight = 987.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.144016 restraints weight = 769.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145430 restraints weight = 647.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2137  Z= 0.126
  Angle     :  0.518   5.349   2938  Z= 0.284
  Chirality :  0.040   0.128    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.701  18.425    311
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.81 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.51), residues: 277
  helix:  2.50 (0.35), residues: 213
  sheet:  None (None), residues: 0
  loop : -1.63 (0.74), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.007   0.001   TYR R 185 
 PHE   0.007   0.001   PHE R 217 
 TRP   0.016   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 2135)
  covalent geometry    : angle       0.51516 ( 2934)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       1.57759 (    4)
  hydrogen bonds       : bond        0.05169 (  161)
  hydrogen bonds       : angle       3.87820 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.051 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6159 (ppp)
REVERT: R  173 TRP cc_start: 0.7775 (m-10) cc_final: 0.6845 (m-90)
  outliers start: 6
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0433
  time to fit residues: 1.7964
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.150200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.133910 restraints weight = 3306.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137224 restraints weight = 1770.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.138780 restraints weight = 1087.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139406 restraints weight = 823.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141083 restraints weight = 700.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.151
  Angle     :  0.551   6.836   2938  Z= 0.302
  Chirality :  0.041   0.124    354
  Planarity :  0.004   0.027    361
  Dihedral  :  4.711  18.600    311
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.34 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.50), residues: 277
  helix:  2.40 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.84 (0.74), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R 217 
 TRP   0.013   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2135)
  covalent geometry    : angle       0.54767 ( 2934)
  SS BOND              : bond        0.00473 (    2)
  SS BOND              : angle       1.69478 (    4)
  hydrogen bonds       : bond        0.05843 (  161)
  hydrogen bonds       : angle       3.99006 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.073 
Fit side-chains
  outliers start: 8
  outliers final: 8
  residues processed: 33
  average time/residue: 0.0579
  time to fit residues: 2.2856
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.152898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136541 restraints weight = 3284.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139759 restraints weight = 1764.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.141349 restraints weight = 1101.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.142094 restraints weight = 833.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.143736 restraints weight = 700.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.151
  Angle     :  0.556   6.760   2938  Z= 0.307
  Chirality :  0.041   0.127    354
  Planarity :  0.003   0.025    361
  Dihedral  :  4.839  19.039    311
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 21.28 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.51), residues: 277
  helix:  2.39 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.78 (0.75), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.008   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R 217 
 TRP   0.007   0.001   TRP R 173 
 HIS   0.003   0.001   HIS R 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2135)
  covalent geometry    : angle       0.55324 ( 2934)
  SS BOND              : bond        0.00455 (    2)
  SS BOND              : angle       1.67945 (    4)
  hydrogen bonds       : bond        0.05866 (  161)
  hydrogen bonds       : angle       3.99519 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.070 
Fit side-chains
REVERT: R  115 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7473 (tp)
REVERT: R  163 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7485 (tt)
REVERT: R  173 TRP cc_start: 0.6724 (m100) cc_final: 0.6008 (m100)
  outliers start: 10
  outliers final: 7
  residues processed: 34
  average time/residue: 0.0605
  time to fit residues: 2.4345
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0670
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.154244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.138008 restraints weight = 3285.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141214 restraints weight = 1750.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.142844 restraints weight = 1079.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143595 restraints weight = 810.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.145087 restraints weight = 676.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
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      :  0.003   0.031   2137  Z= 0.132
  Angle     :  0.518   6.669   2938  Z= 0.285
  Chirality :  0.040   0.125    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.627  18.389    311
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.81 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.51), residues: 277
  helix:  2.40 (0.34), residues: 218
  sheet:  None (None), residues: 0
  loop : -1.56 (0.80), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 131 
 TYR   0.008   0.001   TYR R 174 
 PHE   0.007   0.001   PHE R 217 
 TRP   0.005   0.001   TRP R 158 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2135)
  covalent geometry    : angle       0.51550 ( 2934)
  SS BOND              : bond        0.00421 (    2)
  SS BOND              : angle       1.55389 (    4)
  hydrogen bonds       : bond        0.05221 (  161)
  hydrogen bonds       : angle       3.83721 (  483)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.115 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7560 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0496
  time to fit residues: 1.9708
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.158125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142106 restraints weight = 3338.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.145247 restraints weight = 1727.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147028 restraints weight = 1067.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.147789 restraints weight = 794.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149407 restraints weight = 666.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2137  Z= 0.128
  Angle     :  0.517   6.450   2938  Z= 0.281
  Chirality :  0.040   0.123    354
  Planarity :  0.003   0.025    361
  Dihedral  :  4.522  18.250    311
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.34 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.51), residues: 277
  helix:  2.39 (0.34), residues: 218
  sheet:  None (None), residues: 0
  loop : -1.60 (0.80), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.007   0.001   TYR R 185 
 PHE   0.006   0.001   PHE R 193 
 TRP   0.006   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2135)
  covalent geometry    : angle       0.51382 ( 2934)
  SS BOND              : bond        0.00405 (    2)
  SS BOND              : angle       1.51485 (    4)
  hydrogen bonds       : bond        0.05081 (  161)
  hydrogen bonds       : angle       3.77676 (  483)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 590.42 seconds
wall clock time: 10 minutes 37.99 seconds (637.99 seconds total)