Starting phenix.real_space_refine
on Fri Aug 22 15:08:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8orf_17122/08_2025/8orf_17122.map"
  }
  resolution = 2.5
  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: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1413      2.51       5
     N     420      2.21       5
     O     432      1.98       5
     H    2382      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4653
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 1551
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
  Restraints were copied for chains:
    A, C
  Time building chain proxies: 0.77, per 1000 atoms: 0.17
  Number of scatterers: 4653
  At special positions: 0
  Unit cell: (83.93, 92.65, 35.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     432      8.00
     N     420      7.00
     C    1413      6.00
     H    2382      1.00
    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: 0.34
  Conformation dependent library (CDL) restraints added in 79.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  528

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 45.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283
      removed outlier: 6.421A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299
      removed outlier: 6.432A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310
      removed outlier: 6.822A  pdb=" N   GLY B 304 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLY B 303 " --> pdb=" O   GLY C 304 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   VAL C 306 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   SER B 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE C 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318
      removed outlier: 6.397A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER C 316 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU B 315 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   VAL C 318 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322
      removed outlier: 6.733A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.456A  pdb=" N   ASN B 327 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   HIS C 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   HIS B 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341
      removed outlier: 6.360A  pdb=" N   VAL B 337 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   LYS A 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL B 339 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346
      removed outlier: 6.539A  pdb=" N   ASP B 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354
      removed outlier: 6.272A  pdb=" N   VAL B 350 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   LYS A 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   SER B 352 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361
      removed outlier: 6.632A  pdb=" N   ILE B 360 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 369 through 376
      removed outlier: 6.908A  pdb=" N   LYS B 370 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS A 375 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU B 376 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE C 371 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   GLU B 372 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   THR C 373 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   HIS B 374 " --> pdb=" O   THR C 373 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    144 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: 0.87

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 2376
        1.03 -     1.22: 6
        1.22 -     1.41: 867
        1.41 -     1.61: 1428
        1.61 -     1.80: 6
  Bond restraints: 4683
  Sorted by residual:
  bond pdb=" CG  LYS B 311 "
       pdb=" HG3 LYS B 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CG  LYS C 311 "
       pdb=" HG3 LYS C 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CG  LYS A 311 "
       pdb=" HG3 LYS A 311 "
    ideal  model  delta    sigma   weight residual
    0.970  0.938  0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" CE  LYS A 311 "
       pdb=" NZ  LYS A 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.441  0.048 3.00e-02 1.11e+03 2.58e+00
  bond pdb=" CE  LYS C 311 "
       pdb=" NZ  LYS C 311 "
    ideal  model  delta    sigma   weight residual
    1.489  1.441  0.048 3.00e-02 1.11e+03 2.54e+00
  ... (remaining 4678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 7441
        1.60 -     3.20: 937
        3.20 -     4.80: 151
        4.80 -     6.40: 18
        6.40 -     8.01: 12
  Bond angle restraints: 8559
  Sorted by residual:
  angle pdb=" CA  LYS B 281 "
        pdb=" CB  LYS B 281 "
        pdb=" CG  LYS B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CA  LYS C 281 "
        pdb=" CB  LYS C 281 "
        pdb=" CG  LYS C 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.84   -6.74 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CA  LYS A 281 "
        pdb=" CB  LYS A 281 "
        pdb=" CG  LYS A 281 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" CB  LYS B 280 "
        pdb=" CG  LYS B 280 "
        pdb=" CD  LYS B 280 "
      ideal   model   delta    sigma   weight residual
     111.30  118.92   -7.62 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" N   LYS A 281 "
        pdb=" CA  LYS A 281 "
        pdb=" C   LYS A 281 "
      ideal   model   delta    sigma   weight residual
     109.23  114.36   -5.13 1.55e+00 4.16e-01 1.10e+01
  ... (remaining 8554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.40: 1836
       13.40 -    26.80: 159
       26.80 -    40.20: 45
       40.20 -    53.59: 46
       53.59 -    66.99: 65
  Dihedral angle restraints: 2151
    sinusoidal: 1248
      harmonic: 903
  Sorted by residual:
  dihedral pdb=" CA  SER A 356 "
           pdb=" C   SER A 356 "
           pdb=" N   LEU A 357 "
           pdb=" CA  LEU A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.79   24.21     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  SER B 356 "
           pdb=" C   SER B 356 "
           pdb=" N   LEU B 357 "
           pdb=" CA  LEU B 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  SER C 356 "
           pdb=" C   SER C 356 "
           pdb=" N   LEU C 357 "
           pdb=" CA  LEU C 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.86   24.14     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 2148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 178
       0.049 -    0.098: 128
       0.098 -    0.147: 30
       0.147 -    0.195: 11
       0.195 -    0.244: 4
  Chirality restraints: 351
  Sorted by residual:
  chirality pdb=" CA  LYS A 281 "
            pdb=" N   LYS A 281 "
            pdb=" C   LYS A 281 "
            pdb=" CB  LYS A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  LYS B 281 "
            pdb=" N   LYS B 281 "
            pdb=" C   LYS B 281 "
            pdb=" CB  LYS B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  LYS C 281 "
            pdb=" N   LYS C 281 "
            pdb=" C   LYS C 281 "
            pdb=" CB  LYS C 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 348 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 359 "   -0.035 2.00e-02 2.50e+03   5.29e-02 4.20e+01
        pdb=" CG  ASN C 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 359 "    0.012 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN C 359 "    0.006 2.00e-02 2.50e+03
        pdb="HD22 ASN C 359 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 359 "   -0.035 2.00e-02 2.50e+03   5.26e-02 4.15e+01
        pdb=" CG  ASN B 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 359 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN B 359 "    0.005 2.00e-02 2.50e+03
        pdb="HD22 ASN B 359 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 359 "   -0.035 2.00e-02 2.50e+03   5.25e-02 4.14e+01
        pdb=" CG  ASN A 359 "    0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 359 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 359 "    0.092 2.00e-02 2.50e+03
        pdb="HD21 ASN A 359 "    0.005 2.00e-02 2.50e+03
        pdb="HD22 ASN A 359 "   -0.082 2.00e-02 2.50e+03
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.38: 1978
        2.38 -     2.93: 10703
        2.93 -     3.49: 10615
        3.49 -     4.04: 16031
        4.04 -     4.60: 22249
  Nonbonded interactions: 61576
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 295 "
            pdb=" HZ3 LYS A 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD2 ASP C 295 "
            pdb=" HZ3 LYS C 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD2 ASP B 295 "
            pdb=" HZ3 LYS B 311 "
     model   vdw
     1.823 2.450
  nonbonded pdb=" OD1 ASP B 348 "
            pdb=" H   ARG B 349 "
     model   vdw
     1.882 2.450
  nonbonded pdb=" OD1 ASP C 348 "
            pdb=" H   ARG C 349 "
     model   vdw
     1.882 2.450
  ... (remaining 61571 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}

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:             0.960
  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:             0.020
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.640
  Find NCS groups from input model:        0.030
  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:5.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
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      :  0.010   0.070   2301  Z= 0.375
  Angle     :  1.272   8.005   3078  Z= 0.672
  Chirality :  0.072   0.244    351
  Planarity :  0.005   0.032    393
  Dihedral  : 11.764  65.195    891
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.38), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.29), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.002   ARG B 349 
 TYR   0.015   0.009   TYR A 310 
 PHE   0.011   0.005   PHE B 346 
 HIS   0.018   0.006   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00957 ( 2301)
  covalent geometry    : angle       1.27163 ( 3078)
  hydrogen bonds       : bond        0.11951 (   48)
  hydrogen bonds       : angle       7.54045 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 LYS cc_start: 0.7089 (tptt) cc_final: 0.6750 (mtpt)
REVERT: B  321 LYS cc_start: 0.7757 (mttt) cc_final: 0.7534 (tttm)
REVERT: B  331 LYS cc_start: 0.8230 (mttt) cc_final: 0.7944 (mttt)
REVERT: B  341 SER cc_start: 0.8365 (m) cc_final: 0.8105 (t)
REVERT: A  294 LYS cc_start: 0.8630 (mttt) cc_final: 0.8257 (mttt)
REVERT: A  353 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8177 (ttmm)
REVERT: A  358 ASP cc_start: 0.7447 (t0) cc_final: 0.7180 (t0)
REVERT: A  372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7880 (mt-10)
REVERT: C  294 LYS cc_start: 0.8806 (mttt) cc_final: 0.8306 (mtpt)
REVERT: C  316 SER cc_start: 0.8344 (m) cc_final: 0.8006 (p)
REVERT: C  331 LYS cc_start: 0.8428 (mttt) cc_final: 0.8151 (mttp)
REVERT: C  345 ASP cc_start: 0.7381 (m-30) cc_final: 0.7153 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.9842
  time to fit residues: 117.4467
Evaluate side-chains
  72 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN
B 286 ASN
B 336 GLN
C 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.153393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.138060 restraints weight = 7859.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.93
r_work: 0.4051 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3957 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2301  Z= 0.122
  Angle     :  0.605   5.002   3078  Z= 0.307
  Chirality :  0.051   0.136    351
  Planarity :  0.003   0.028    393
  Dihedral  :  6.916  18.435    306
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.29 %
    Favored  : 81.06 %
  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 aren not related in a simple way.
  whole: -3.14 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG B 349 
 TYR   0.005   0.001   TYR C 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.006   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2301)
  covalent geometry    : angle       0.60475 ( 3078)
  hydrogen bonds       : bond        0.02526 (   48)
  hydrogen bonds       : angle       5.90780 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8524 (mt0) cc_final: 0.8180 (mt0)
REVERT: B  341 SER cc_start: 0.8662 (m) cc_final: 0.8353 (t)
REVERT: B  343 LYS cc_start: 0.8428 (mttt) cc_final: 0.8152 (tptp)
REVERT: B  369 LYS cc_start: 0.8033 (mttt) cc_final: 0.7581 (ttmt)
REVERT: A  353 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8531 (ttmm)
REVERT: A  369 LYS cc_start: 0.8343 (mttt) cc_final: 0.7960 (ttmt)
REVERT: C  341 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8468 (t)
REVERT: C  369 LYS cc_start: 0.8283 (mttt) cc_final: 0.7792 (ttpt)
  outliers start: 7
  outliers final: 3
  residues processed: 75
  average time/residue: 0.8623
  time to fit residues: 66.2222
Evaluate side-chains
  69 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  345 ASP
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  341 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN
C 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.139883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.126526 restraints weight = 8476.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 1.75
r_work: 0.3913 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3819 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2301  Z= 0.165
  Angle     :  0.584   5.079   3078  Z= 0.296
  Chirality :  0.051   0.133    351
  Planarity :  0.004   0.024    393
  Dihedral  :  6.454  17.924    306
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.56 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.005   0.001   TYR A 310 
 PHE   0.005   0.001   PHE C 346 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2301)
  covalent geometry    : angle       0.58410 ( 3078)
  hydrogen bonds       : bond        0.02395 (   48)
  hydrogen bonds       : angle       5.28819 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 SER cc_start: 0.8646 (m) cc_final: 0.8416 (t)
REVERT: B  369 LYS cc_start: 0.8115 (mttt) cc_final: 0.7675 (ttmt)
REVERT: A  369 LYS cc_start: 0.8461 (mttt) cc_final: 0.8168 (ttmt)
REVERT: C  317 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (tttp)
REVERT: C  369 LYS cc_start: 0.8271 (mttt) cc_final: 0.7808 (ttpt)
  outliers start: 9
  outliers final: 2
  residues processed: 70
  average time/residue: 0.7945
  time to fit residues: 57.0125
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0670
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.140959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.127542 restraints weight = 8678.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.78
r_work: 0.3952 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3861 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.5637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2301  Z= 0.148
  Angle     :  0.576   5.072   3078  Z= 0.291
  Chirality :  0.051   0.131    351
  Planarity :  0.004   0.026    393
  Dihedral  :  6.236  18.234    306
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.21 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.36), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.005   0.001   TYR A 310 
 PHE   0.006   0.001   PHE C 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2301)
  covalent geometry    : angle       0.57609 ( 3078)
  hydrogen bonds       : bond        0.02074 (   48)
  hydrogen bonds       : angle       5.04769 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8546 (mt0) cc_final: 0.8207 (mt0)
REVERT: B  341 SER cc_start: 0.8695 (m) cc_final: 0.8457 (t)
REVERT: B  369 LYS cc_start: 0.8198 (mttt) cc_final: 0.7767 (ttmt)
REVERT: A  358 ASP cc_start: 0.7152 (t70) cc_final: 0.6929 (t0)
REVERT: A  369 LYS cc_start: 0.8523 (mttt) cc_final: 0.8205 (ttmt)
REVERT: C  317 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (tttp)
REVERT: C  336 GLN cc_start: 0.8536 (mt0) cc_final: 0.8163 (mt0)
REVERT: C  369 LYS cc_start: 0.8247 (mttt) cc_final: 0.7831 (ttpt)
  outliers start: 4
  outliers final: 2
  residues processed: 67
  average time/residue: 0.7654
  time to fit residues: 52.6596
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
A 362 HIS
C 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.140657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.127219 restraints weight = 8545.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 1.77
r_work: 0.3940 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.5881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2301  Z= 0.142
  Angle     :  0.561   4.961   3078  Z= 0.282
  Chirality :  0.051   0.131    351
  Planarity :  0.004   0.027    393
  Dihedral  :  6.027  18.976    306
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.70 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.005   0.001   TYR A 310 
 PHE   0.003   0.001   PHE C 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 2301)
  covalent geometry    : angle       0.56101 ( 3078)
  hydrogen bonds       : bond        0.01888 (   48)
  hydrogen bonds       : angle       4.84985 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 SER cc_start: 0.8646 (m) cc_final: 0.8389 (t)
REVERT: B  369 LYS cc_start: 0.8157 (mttt) cc_final: 0.7769 (ttmt)
REVERT: A  369 LYS cc_start: 0.8523 (mttt) cc_final: 0.8228 (ttmt)
REVERT: C  317 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8673 (tttp)
REVERT: C  336 GLN cc_start: 0.8508 (mt0) cc_final: 0.8276 (mt0)
REVERT: C  369 LYS cc_start: 0.8262 (mttt) cc_final: 0.7859 (ttpt)
  outliers start: 6
  outliers final: 3
  residues processed: 66
  average time/residue: 0.8842
  time to fit residues: 59.7716
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.144130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.130625 restraints weight = 8609.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 1.77
r_work: 0.3975 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3885 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.6170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2301  Z= 0.111
  Angle     :  0.539   4.833   3078  Z= 0.271
  Chirality :  0.050   0.130    351
  Planarity :  0.004   0.025    393
  Dihedral  :  5.782  19.115    306
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.32 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.002   0.001   PHE C 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2301)
  covalent geometry    : angle       0.53851 ( 3078)
  hydrogen bonds       : bond        0.01665 (   48)
  hydrogen bonds       : angle       4.67614 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8593 (mt0) cc_final: 0.8223 (mt0)
REVERT: B  341 SER cc_start: 0.8555 (m) cc_final: 0.8339 (t)
REVERT: B  369 LYS cc_start: 0.8131 (mttt) cc_final: 0.7841 (ttmt)
REVERT: A  343 LYS cc_start: 0.8641 (tttp) cc_final: 0.8151 (ttpt)
REVERT: A  369 LYS cc_start: 0.8463 (mttt) cc_final: 0.8212 (ttmt)
REVERT: C  336 GLN cc_start: 0.8458 (mt0) cc_final: 0.8108 (mt0)
REVERT: C  369 LYS cc_start: 0.8237 (mttt) cc_final: 0.7833 (tttt)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.8249
  time to fit residues: 57.6102
Evaluate side-chains
  65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.142996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.129728 restraints weight = 8554.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 1.75
r_work: 0.3979 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.6259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2301  Z= 0.114
  Angle     :  0.526   5.145   3078  Z= 0.265
  Chirality :  0.050   0.130    351
  Planarity :  0.004   0.026    393
  Dihedral  :  5.653  20.114    306
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.70 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.002   0.001   PHE C 346 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 2301)
  covalent geometry    : angle       0.52584 ( 3078)
  hydrogen bonds       : bond        0.01586 (   48)
  hydrogen bonds       : angle       4.61624 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8213 (mttt) cc_final: 0.7864 (ttmt)
REVERT: A  369 LYS cc_start: 0.8443 (mttt) cc_final: 0.8216 (ttmt)
REVERT: C  369 LYS cc_start: 0.8263 (mttt) cc_final: 0.7861 (ttpt)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.8546
  time to fit residues: 56.8985
Evaluate side-chains
  61 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 336 GLN
C 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.141533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.128138 restraints weight = 8687.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 1.76
r_work: 0.3957 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3869 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2301  Z= 0.126
  Angle     :  0.525   4.951   3078  Z= 0.267
  Chirality :  0.050   0.130    351
  Planarity :  0.004   0.028    393
  Dihedral  :  5.677  20.483    306
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.21 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.45 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.002   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2301)
  covalent geometry    : angle       0.52489 ( 3078)
  hydrogen bonds       : bond        0.01613 (   48)
  hydrogen bonds       : angle       4.68237 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8631 (mt0) cc_final: 0.8262 (mt0)
REVERT: B  369 LYS cc_start: 0.8241 (mttt) cc_final: 0.7900 (ttmt)
REVERT: A  281 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (tttp)
REVERT: A  369 LYS cc_start: 0.8457 (mttt) cc_final: 0.8246 (ttmt)
REVERT: C  369 LYS cc_start: 0.8270 (mttt) cc_final: 0.7867 (ttpt)
  outliers start: 5
  outliers final: 3
  residues processed: 63
  average time/residue: 0.7729
  time to fit residues: 49.9816
Evaluate side-chains
  62 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 18 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.142349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.129067 restraints weight = 8385.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 1.72
r_work: 0.3970 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3882 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.6388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2301  Z= 0.120
  Angle     :  0.515   5.122   3078  Z= 0.262
  Chirality :  0.050   0.129    351
  Planarity :  0.004   0.028    393
  Dihedral  :  5.618  20.957    306
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.45 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.48 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.002   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2301)
  covalent geometry    : angle       0.51539 ( 3078)
  hydrogen bonds       : bond        0.01593 (   48)
  hydrogen bonds       : angle       4.64717 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 LYS cc_start: 0.8231 (mttt) cc_final: 0.7886 (ttmt)
REVERT: A  281 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8316 (tttp)
REVERT: A  369 LYS cc_start: 0.8420 (mttt) cc_final: 0.8210 (ttmt)
REVERT: C  369 LYS cc_start: 0.8332 (mttt) cc_final: 0.7905 (ttpt)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.8524
  time to fit residues: 54.2355
Evaluate side-chains
  63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
C 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.142791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.129345 restraints weight = 8567.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 1.74
r_work: 0.3964 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.6397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2301  Z= 0.117
  Angle     :  0.520   5.042   3078  Z= 0.266
  Chirality :  0.050   0.130    351
  Planarity :  0.004   0.028    393
  Dihedral  :  5.573  21.129    306
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.45 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.47 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.004   0.001   TYR A 310 
 PHE   0.002   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2301)
  covalent geometry    : angle       0.52027 ( 3078)
  hydrogen bonds       : bond        0.01524 (   48)
  hydrogen bonds       : angle       4.62142 (  144)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  336 GLN cc_start: 0.8600 (mt0) cc_final: 0.8239 (mt0)
REVERT: B  369 LYS cc_start: 0.8254 (mttt) cc_final: 0.7956 (ttmt)
REVERT: A  369 LYS cc_start: 0.8424 (mttt) cc_final: 0.8213 (ttmt)
REVERT: C  369 LYS cc_start: 0.8346 (mttt) cc_final: 0.7915 (ttpt)
  outliers start: 6
  outliers final: 3
  residues processed: 62
  average time/residue: 0.7085
  time to fit residues: 45.1469
Evaluate side-chains
  60 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.145657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.132317 restraints weight = 8504.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 1.73
r_work: 0.4015 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3931 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.6536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2301  Z= 0.094
  Angle     :  0.507   4.792   3078  Z= 0.257
  Chirality :  0.051   0.129    351
  Planarity :  0.004   0.029    393
  Dihedral  :  5.375  20.966    306
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.59 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.50 (0.37), residues: 297
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.28), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.003   0.001   TYR C 310 
 PHE   0.001   0.000   PHE A 346 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2301)
  covalent geometry    : angle       0.50718 ( 3078)
  hydrogen bonds       : bond        0.01426 (   48)
  hydrogen bonds       : angle       4.53690 (  144)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2419.10 seconds
wall clock time: 41 minutes 39.26 seconds (2499.26 seconds total)