Starting phenix.real_space_refine
on Tue Mar  3 10:49:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2026/7py2_13708.cif"
  }
  resolution = 2.59
  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=   0.004
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      32      5.16       5
     C    1264      2.51       5
     N     420      2.21       5
     O     436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 2152
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 538
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 2, 'TRANS': 76}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 0.39, per 1000 atoms: 0.18
  Number of scatterers: 2152
  At special positions: 0
  Unit cell: (79.05, 67.89, 40.92, 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      32     16.00
     O     436      8.00
     N     420      7.00
     C    1264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.10
  Conformation dependent library (CDL) restraints added in 66.0 milliseconds
  

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  472

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 283 through 285
      removed outlier: 6.524A  pdb=" N   GLY A 284 " --> pdb=" O   ASN B 285 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLY C 284 " --> pdb=" O   ASN D 285 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 298 through 299
      removed outlier: 5.853A  pdb=" N   GLY A 298 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   GLY C 298 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 302 through 303
      removed outlier: 6.660A  pdb=" N   ASN A 302 " --> pdb=" O   GLN D 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 313
      removed outlier: 6.669A  pdb=" N   ASN A 312 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN C 312 " --> pdb=" O   PHE D 313 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329
      removed outlier: 8.352A  pdb=" N   GLN A 327 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ALA D 329 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   GLN C 327 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 343
      removed outlier: 6.920A  pdb=" N   GLN B 343 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   SER A 333 " --> pdb=" O   TRP D 334 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   MET D 336 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLY A 335 " --> pdb=" O   MET D 336 " (cutoff:3.500A)
      removed outlier: 8.260A  pdb=" N   GLY D 338 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   MET A 337 " --> pdb=" O   GLY D 338 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   LEU D 340 " --> pdb=" O   MET A 337 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   MET A 339 " --> pdb=" O   LEU D 340 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   SER D 342 " --> pdb=" O   MET A 339 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   ALA A 341 " --> pdb=" O   SER D 342 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLN D 343 " --> pdb=" O   SER C 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 347
      removed outlier: 6.744A  pdb=" N   GLN A 346 " --> pdb=" O   SER D 347 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 356
      removed outlier: 6.897A  pdb=" N   GLN A 354 " --> pdb=" O   ASN D 355 " (cutoff:3.500A)

    32 hydrogen bonds defined for protein.
    96 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: 0.19

  Time building geometry restraints manager: 0.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 662
        1.34 -     1.46: 325
        1.46 -     1.59: 1129
        1.59 -     1.71: 0
        1.71 -     1.83: 64
  Bond restraints: 2180
  Sorted by residual:
  bond pdb=" C   ALA C 321 "
       pdb=" O   ALA C 321 "
    ideal  model  delta    sigma   weight residual
    1.232  1.292 -0.060 1.34e-02 5.57e+03 2.00e+01
  bond pdb=" C   ALA D 321 "
       pdb=" O   ALA D 321 "
    ideal  model  delta    sigma   weight residual
    1.232  1.291 -0.060 1.34e-02 5.57e+03 2.00e+01
  bond pdb=" C   ALA A 321 "
       pdb=" O   ALA A 321 "
    ideal  model  delta    sigma   weight residual
    1.232  1.291 -0.060 1.34e-02 5.57e+03 1.98e+01
  bond pdb=" C   ALA B 321 "
       pdb=" O   ALA B 321 "
    ideal  model  delta    sigma   weight residual
    1.232  1.291 -0.059 1.34e-02 5.57e+03 1.96e+01
  bond pdb=" N   GLY A 348 "
       pdb=" CA  GLY A 348 "
    ideal  model  delta    sigma   weight residual
    1.434  1.477 -0.044 1.22e-02 6.72e+03 1.28e+01
  ... (remaining 2175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 1641
        1.39 -     2.79: 893
        2.79 -     4.18: 278
        4.18 -     5.58: 68
        5.58 -     6.97: 20
  Bond angle restraints: 2900
  Sorted by residual:
  angle pdb=" C   ARG D 293 "
        pdb=" N   GLY D 294 "
        pdb=" CA  GLY D 294 "
      ideal   model   delta    sigma   weight residual
     119.92  124.57   -4.65 9.60e-01 1.09e+00 2.35e+01
  angle pdb=" C   ARG A 293 "
        pdb=" N   GLY A 294 "
        pdb=" CA  GLY A 294 "
      ideal   model   delta    sigma   weight residual
     119.92  124.55   -4.63 9.60e-01 1.09e+00 2.33e+01
  angle pdb=" C   ARG C 293 "
        pdb=" N   GLY C 294 "
        pdb=" CA  GLY C 294 "
      ideal   model   delta    sigma   weight residual
     119.92  124.55   -4.63 9.60e-01 1.09e+00 2.33e+01
  angle pdb=" C   ARG B 293 "
        pdb=" N   GLY B 294 "
        pdb=" CA  GLY B 294 "
      ideal   model   delta    sigma   weight residual
     119.92  124.53   -4.61 9.60e-01 1.09e+00 2.30e+01
  angle pdb=" C   LEU B 330 "
        pdb=" N   GLN B 331 "
        pdb=" CA  GLN B 331 "
      ideal   model   delta    sigma   weight residual
     122.34  128.90   -6.56 1.39e+00 5.18e-01 2.23e+01
  ... (remaining 2895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.20: 1080
       17.20 -    34.38: 116
       34.38 -    51.57: 36
       51.57 -    68.76: 4
       68.76 -    85.95: 8
  Dihedral angle restraints: 1244
    sinusoidal: 460
      harmonic: 784
  Sorted by residual:
  dihedral pdb=" CA  GLY B 284 "
           pdb=" C   GLY B 284 "
           pdb=" N   ASN B 285 "
           pdb=" CA  ASN B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.83  -21.17     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLY D 284 "
           pdb=" C   GLY D 284 "
           pdb=" N   ASN D 285 "
           pdb=" CA  ASN D 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLY A 284 "
           pdb=" C   GLY A 284 "
           pdb=" N   ASN A 285 "
           pdb=" CA  ASN A 285 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 1241 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 102
       0.044 -    0.088: 82
       0.088 -    0.132: 48
       0.132 -    0.176: 16
       0.176 -    0.220: 4
  Chirality restraints: 252
  Sorted by residual:
  chirality pdb=" CA  ILE B 318 "
            pdb=" N   ILE B 318 "
            pdb=" C   ILE B 318 "
            pdb=" CB  ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE A 318 "
            pdb=" N   ILE A 318 "
            pdb=" C   ILE A 318 "
            pdb=" CB  ILE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE D 318 "
            pdb=" N   ILE D 318 "
            pdb=" C   ILE D 318 "
            pdb=" CB  ILE D 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 249 not shown)

  Planarity restraints: 432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 336 "   -0.009 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" C   MET C 336 "    0.033 2.00e-02 2.50e+03
        pdb=" O   MET C 336 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET C 337 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET D 336 "   -0.009 2.00e-02 2.50e+03   1.93e-02 3.72e+00
        pdb=" C   MET D 336 "    0.033 2.00e-02 2.50e+03
        pdb=" O   MET D 336 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET D 337 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 336 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" C   MET A 336 "    0.033 2.00e-02 2.50e+03
        pdb=" O   MET A 336 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   MET A 337 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 429 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 761
        2.92 -     3.41: 2046
        3.41 -     3.91: 3535
        3.91 -     4.40: 4076
        4.40 -     4.90: 7455
  Nonbonded interactions: 17873
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 355 "
            pdb=" ND2 ASN D 358 "
     model   vdw
     2.423 3.120
  nonbonded pdb=" ND2 ASN A 358 "
            pdb=" O   ASN D 355 "
     model   vdw
     2.423 3.120
  nonbonded pdb=" O   ASN A 355 "
            pdb=" ND2 ASN B 358 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" OG  SER A 333 "
            pdb=" O   GLY B 300 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" O   GLY A 300 "
            pdb=" OG  SER D 333 "
     model   vdw
     2.559 3.040
  ... (remaining 17868 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.510
  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:5.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
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      :  0.015   0.060   2180  Z= 1.113
  Angle     :  1.835   6.975   2900  Z= 1.282
  Chirality :  0.079   0.220    252
  Planarity :  0.007   0.019    432
  Dihedral  : 17.258  85.948    772
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  8.00 %
    Favored  : 90.00 %
  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: -5.22 (0.22), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 293 
 PHE   0.017   0.006   PHE D 289 
 TRP   0.012   0.004   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01508 ( 2180)
  covalent geometry    : angle       1.83468 ( 2900)
  hydrogen bonds       : bond        0.16093 (   32)
  hydrogen bonds       : angle       6.42247 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8336 (mmt90)
REVERT: A  339 MET cc_start: 0.8144 (ttt) cc_final: 0.7914 (ttp)
REVERT: B  359 MET cc_start: 0.8258 (ttt) cc_final: 0.8030 (mtp)
REVERT: C  293 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8543 (mtt-85)
  outliers start: 4
  outliers final: 0
  residues processed: 68
  average time/residue: 0.7158
  time to fit residues: 49.3962
Evaluate side-chains
  51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
C 346 GLN
D 286 GLN
D 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.109515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.098692 restraints weight = 2421.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.60
r_work: 0.3394 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2180  Z= 0.128
  Angle     :  0.599   4.343   2900  Z= 0.326
  Chirality :  0.041   0.123    252
  Planarity :  0.003   0.022    432
  Dihedral  :  5.303  14.773    316
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 18.50 %
    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: -4.63 (0.22), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 293 
 PHE   0.011   0.002   PHE A 313 
 TRP   0.013   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2180)
  covalent geometry    : angle       0.59950 ( 2900)
  hydrogen bonds       : bond        0.01633 (   32)
  hydrogen bonds       : angle       4.29157 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7970 (mmt90)
REVERT: A  356 GLN cc_start: 0.8169 (mt0) cc_final: 0.7786 (mt0)
REVERT: B  359 MET cc_start: 0.7850 (ttt) cc_final: 0.7633 (mtp)
  outliers start: 13
  outliers final: 4
  residues processed: 59
  average time/residue: 0.7271
  time to fit residues: 43.5126
Evaluate side-chains
  56 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain C residue  311 MET
Chi-restraints excluded: chain C residue  342 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
C 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.101913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.090875 restraints weight = 2476.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.60
r_work: 0.3306 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2180  Z= 0.211
  Angle     :  0.681   4.802   2900  Z= 0.373
  Chirality :  0.047   0.132    252
  Planarity :  0.003   0.023    432
  Dihedral  :  5.169  15.413    316
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 20.00 %
    Favored  : 74.50 %
  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: -4.33 (0.22), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 293 
 PHE   0.011   0.002   PHE B 283 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 2180)
  covalent geometry    : angle       0.68068 ( 2900)
  hydrogen bonds       : bond        0.02469 (   32)
  hydrogen bonds       : angle       4.55587 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.071 
Fit side-chains
REVERT: B  293 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7837 (mmt90)
REVERT: B  337 MET cc_start: 0.8947 (ttm) cc_final: 0.8684 (ttm)
  outliers start: 11
  outliers final: 1
  residues processed: 61
  average time/residue: 0.8141
  time to fit residues: 50.3206
Evaluate side-chains
  58 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain B residue  350 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 303 GLN
A 354 GLN
B 354 GLN
D 354 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.101136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.090318 restraints weight = 2397.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.57
r_work: 0.3284 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2180  Z= 0.195
  Angle     :  0.659   4.591   2900  Z= 0.360
  Chirality :  0.046   0.124    252
  Planarity :  0.003   0.020    432
  Dihedral  :  5.141  15.938    316
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 15.50 %
    Favored  : 77.00 %
  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: -4.17 (0.22), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 293 
 PHE   0.008   0.002   PHE B 283 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 2180)
  covalent geometry    : angle       0.65925 ( 2900)
  hydrogen bonds       : bond        0.02329 (   32)
  hydrogen bonds       : angle       4.55991 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.074 
Fit side-chains
REVERT: B  293 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7860 (mmt90)
REVERT: B  337 MET cc_start: 0.8960 (ttm) cc_final: 0.8721 (ttm)
  outliers start: 15
  outliers final: 6
  residues processed: 61
  average time/residue: 0.7265
  time to fit residues: 44.9391
Evaluate side-chains
  62 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Chi-restraints excluded: chain D residue  354 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 354 GLN
D 354 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.098565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.087804 restraints weight = 2517.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.59
r_work: 0.3248 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   2180  Z= 0.319
  Angle     :  0.773   5.489   2900  Z= 0.424
  Chirality :  0.051   0.129    252
  Planarity :  0.004   0.021    432
  Dihedral  :  5.394  15.308    316
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 18.00 %
    Favored  : 76.00 %
  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: -4.13 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 293 
 PHE   0.010   0.002   PHE B 283 
 TRP   0.016   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 2180)
  covalent geometry    : angle       0.77334 ( 2900)
  hydrogen bonds       : bond        0.02994 (   32)
  hydrogen bonds       : angle       4.71874 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8985 (ttm) cc_final: 0.8751 (ttm)
  outliers start: 12
  outliers final: 4
  residues processed: 59
  average time/residue: 0.7457
  time to fit residues: 44.6314
Evaluate side-chains
  57 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 354 GLN
D 303 GLN
D 354 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.089400 restraints weight = 2453.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.57
r_work: 0.3276 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2180  Z= 0.206
  Angle     :  0.674   4.552   2900  Z= 0.368
  Chirality :  0.046   0.126    252
  Planarity :  0.003   0.020    432
  Dihedral  :  5.249  15.933    316
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 19.00 %
    Favored  : 75.50 %
  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: -4.10 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG A 293 
 PHE   0.008   0.002   PHE B 289 
 TRP   0.015   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 2180)
  covalent geometry    : angle       0.67380 ( 2900)
  hydrogen bonds       : bond        0.02362 (   32)
  hydrogen bonds       : angle       4.70145 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.046 
Fit side-chains
REVERT: B  293 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7928 (mmt90)
REVERT: B  337 MET cc_start: 0.8961 (ttm) cc_final: 0.8728 (ttm)
  outliers start: 11
  outliers final: 4
  residues processed: 61
  average time/residue: 0.6329
  time to fit residues: 39.1373
Evaluate side-chains
  60 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 354 GLN
D 303 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.100528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.089696 restraints weight = 2427.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.58
r_work: 0.3282 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2180  Z= 0.177
  Angle     :  0.644   4.322   2900  Z= 0.351
  Chirality :  0.045   0.124    252
  Planarity :  0.003   0.018    432
  Dihedral  :  5.127  15.607    316
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 18.50 %
    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: -4.07 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 PHE   0.007   0.001   PHE B 289 
 TRP   0.015   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 2180)
  covalent geometry    : angle       0.64447 ( 2900)
  hydrogen bonds       : bond        0.02173 (   32)
  hydrogen bonds       : angle       4.71144 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.081 
Fit side-chains
REVERT: B  293 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7934 (mmt90)
REVERT: B  337 MET cc_start: 0.8953 (ttm) cc_final: 0.8718 (ttm)
  outliers start: 13
  outliers final: 4
  residues processed: 61
  average time/residue: 0.6375
  time to fit residues: 39.4848
Evaluate side-chains
  61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
B 354 GLN
D 303 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.101736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.090821 restraints weight = 2475.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.60
r_work: 0.3302 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2180  Z= 0.154
  Angle     :  0.623   4.048   2900  Z= 0.338
  Chirality :  0.044   0.123    252
  Planarity :  0.003   0.018    432
  Dihedral  :  5.006  14.920    316
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 19.00 %
    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: -4.03 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 PHE   0.007   0.001   PHE B 289 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2180)
  covalent geometry    : angle       0.62336 ( 2900)
  hydrogen bonds       : bond        0.01931 (   32)
  hydrogen bonds       : angle       4.72283 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.071 
Fit side-chains
REVERT: B  293 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7958 (mmt90)
REVERT: B  337 MET cc_start: 0.8936 (ttm) cc_final: 0.8717 (ttm)
REVERT: D  330 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8635 (tt)
  outliers start: 12
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5831
  time to fit residues: 38.4663
Evaluate side-chains
  63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 354 GLN
B 354 GLN
C 354 GLN
D 303 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.100675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089629 restraints weight = 2467.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.61
r_work: 0.3292 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2180  Z= 0.172
  Angle     :  0.647   4.251   2900  Z= 0.349
  Chirality :  0.044   0.124    252
  Planarity :  0.003   0.018    432
  Dihedral  :  5.000  14.572    316
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 20.00 %
    Favored  : 74.00 %
  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: -3.99 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 PHE   0.008   0.001   PHE B 289 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 2180)
  covalent geometry    : angle       0.64674 ( 2900)
  hydrogen bonds       : bond        0.02094 (   32)
  hydrogen bonds       : angle       4.75970 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  307 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9059 (mtp)
REVERT: B  293 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7975 (mmt90)
REVERT: B  337 MET cc_start: 0.8958 (ttm) cc_final: 0.8718 (ttm)
  outliers start: 12
  outliers final: 5
  residues processed: 61
  average time/residue: 0.5957
  time to fit residues: 36.8880
Evaluate side-chains
  63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  354 GLN
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 354 GLN
B 354 GLN
D 303 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.100632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.089730 restraints weight = 2508.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.61
r_work: 0.3293 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2180  Z= 0.175
  Angle     :  0.652   4.155   2900  Z= 0.351
  Chirality :  0.045   0.126    252
  Planarity :  0.003   0.018    432
  Dihedral  :  4.993  14.384    316
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 22.00 %
    Favored  : 74.00 %
  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: -3.98 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.17), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 PHE   0.008   0.001   PHE B 289 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 2180)
  covalent geometry    : angle       0.65214 ( 2900)
  hydrogen bonds       : bond        0.02198 (   32)
  hydrogen bonds       : angle       4.79353 (   96)

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

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

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  616 Ramachandran restraints generated.
    308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.073 
Fit side-chains
REVERT: A  307 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9045 (mtp)
REVERT: B  293 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7986 (mmt90)
REVERT: B  337 MET cc_start: 0.8957 (ttm) cc_final: 0.8724 (ttm)
  outliers start: 8
  outliers final: 4
  residues processed: 58
  average time/residue: 0.6794
  time to fit residues: 39.9403
Evaluate side-chains
  62 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue  293 ARG
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain D residue  350 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0570
   chunk 13 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    4.2106

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 354 GLN
B 354 GLN
D 303 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.099690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088671 restraints weight = 2546.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.63
r_work: 0.3274 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2180  Z= 0.237
  Angle     :  0.709   4.633   2900  Z= 0.384
  Chirality :  0.048   0.135    252
  Planarity :  0.003   0.018    432
  Dihedral  :  5.143  15.331    316
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 19.50 %
    Favored  : 75.50 %
  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: -3.96 (0.23), residues: 308
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.18), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 PHE   0.009   0.002   PHE B 283 
 TRP   0.014   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 2180)
  covalent geometry    : angle       0.70854 ( 2900)
  hydrogen bonds       : bond        0.02500 (   32)
  hydrogen bonds       : angle       4.85696 (   96)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1146.62 seconds
wall clock time: 20 minutes 31.59 seconds (1231.59 seconds total)