Starting phenix.real_space_refine
on Wed Sep 17 08:28:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bxi_45005/09_2025/9bxi_45005.map"
  }
  resolution = 2.7
  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=   0.003
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    2202      2.51       5
     N     648      2.21       5
     O     672      1.98       5
     H    3654      0.53       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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7182
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.25, per 1000 atoms: 0.17
  Number of scatterers: 7182
  At special positions: 0
  Unit cell: (81.732, 159.294, 37.53, 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     672      8.00
     N     648      7.00
     C    2202      6.00
     H    3654      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: 0.72
  Conformation dependent library (CDL) restraints added in 282.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  804

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322
      removed outlier: 6.506A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL C 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   LYS E 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   SER C 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.422A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE C 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356
      removed outlier: 6.807A  pdb=" N   SER A 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER C 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
      removed outlier: 6.468A  pdb=" N   ASN A 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   HIS C 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ASN C 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   HIS E 362 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR C 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375
    Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310
    Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322
      removed outlier: 6.498A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL D 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 8.544A  pdb=" N   LYS F 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   SER D 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.423A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ILE D 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340
    Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346
    Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356
      removed outlier: 6.824A  pdb=" N   SER B 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   SER D 356 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362
      removed outlier: 6.488A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASN D 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   HIS F 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375

    92 hydrogen bonds defined for protein.
    276 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: 1.46

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3648
        1.12 -     1.29: 600
        1.29 -     1.46: 1045
        1.46 -     1.63: 1937
        1.63 -     1.80: 6
  Bond restraints: 7236
  Sorted by residual:
  bond pdb=" N   SER D 305 "
       pdb=" H   SER D 305 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.77e+01
  bond pdb=" N   SER F 305 "
       pdb=" H   SER F 305 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   SER B 305 "
       pdb=" H   SER B 305 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   LYS B 331 "
       pdb=" H   LYS B 331 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   LYS F 331 "
       pdb=" H   LYS F 331 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 7231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 11365
        2.50 -     5.00: 1325
        5.00 -     7.49: 474
        7.49 -     9.99: 18
        9.99 -    12.49: 6
  Bond angle restraints: 13188
  Sorted by residual:
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.79   -4.99 1.00e+00 1.00e+00 2.49e+01
  angle pdb=" CA  PHE C 346 "
        pdb=" CB  PHE C 346 "
        pdb=" CG  PHE C 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.76   -4.96 1.00e+00 1.00e+00 2.46e+01
  angle pdb=" CA  PHE F 346 "
        pdb=" CB  PHE F 346 "
        pdb=" CG  PHE F 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.76   -4.96 1.00e+00 1.00e+00 2.46e+01
  angle pdb=" CA  PHE A 346 "
        pdb=" CB  PHE A 346 "
        pdb=" CG  PHE A 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.74   -4.94 1.00e+00 1.00e+00 2.44e+01
  angle pdb=" CA  PHE D 346 "
        pdb=" CB  PHE D 346 "
        pdb=" CG  PHE D 346 "
      ideal   model   delta    sigma   weight residual
     113.80  118.73   -4.93 1.00e+00 1.00e+00 2.43e+01
  ... (remaining 13183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.99: 2982
       13.99 -    27.97: 144
       27.97 -    41.96: 72
       41.96 -    55.94: 54
       55.94 -    69.93: 72
  Dihedral angle restraints: 3324
    sinusoidal: 1902
      harmonic: 1422
  Sorted by residual:
  dihedral pdb=" CA  GLN B 351 "
           pdb=" C   GLN B 351 "
           pdb=" N   SER B 352 "
           pdb=" CA  SER B 352 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.18  -16.82     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  GLN D 351 "
           pdb=" C   GLN D 351 "
           pdb=" N   SER D 352 "
           pdb=" CA  SER D 352 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.19  -16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  GLN A 351 "
           pdb=" C   GLN A 351 "
           pdb=" N   SER A 352 "
           pdb=" CA  SER A 352 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.21  -16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 3321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.053: 281
       0.053 -    0.105: 163
       0.105 -    0.157: 72
       0.157 -    0.209: 12
       0.209 -    0.261: 6
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  ARG D 349 "
            pdb=" N   ARG D 349 "
            pdb=" C   ARG D 349 "
            pdb=" CB  ARG D 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  ARG B 349 "
            pdb=" N   ARG B 349 "
            pdb=" C   ARG B 349 "
            pdb=" CB  ARG B 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ARG A 349 "
            pdb=" N   ARG A 349 "
            pdb=" C   ARG A 349 "
            pdb=" CB  ARG A 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 531 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 360 "   -0.020 2.00e-02 2.50e+03   3.68e-02 1.36e+01
        pdb=" N   THR A 361 "    0.064 2.00e-02 2.50e+03
        pdb=" CA  THR A 361 "   -0.018 2.00e-02 2.50e+03
        pdb=" H   THR A 361 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 360 "    0.020 2.00e-02 2.50e+03   3.68e-02 1.36e+01
        pdb=" N   THR D 361 "   -0.064 2.00e-02 2.50e+03
        pdb=" CA  THR D 361 "    0.018 2.00e-02 2.50e+03
        pdb=" H   THR D 361 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 360 "    0.020 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" N   THR B 361 "   -0.064 2.00e-02 2.50e+03
        pdb=" CA  THR B 361 "    0.018 2.00e-02 2.50e+03
        pdb=" H   THR B 361 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        0.59 -     1.40: 61
        1.40 -     2.20: 778
        2.20 -     3.00: 18727
        3.00 -     3.80: 28293
        3.80 -     4.60: 44416
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 92275
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 370 "
            pdb=" HG  SER D 316 "
     model   vdw
     0.594 2.600
  nonbonded pdb=" NZ  LYS C 370 "
            pdb=" HG  SER E 316 "
     model   vdw
     0.603 2.600
  nonbonded pdb=" NZ  LYS D 370 "
            pdb=" HG  SER F 316 "
     model   vdw
     0.607 2.600
  nonbonded pdb=" NZ  LYS A 370 "
            pdb=" HG  SER C 316 "
     model   vdw
     0.632 2.600
  nonbonded pdb=" HZ1 LYS A 370 "
            pdb=" HG  SER C 316 "
     model   vdw
     0.734 2.100
  ... (remaining 92270 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.490
  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:             0.050
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
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   0.041   3582  Z= 0.614
  Angle     :  1.608   5.507   4794  Z= 1.016
  Chirality :  0.078   0.261    534
  Planarity :  0.006   0.017    618
  Dihedral  : 10.278  69.928   1380
  Min Nonbonded Distance : 1.231

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.011   0.005   TYR B 310 
 PHE   0.017   0.006   PHE E 346 
 HIS   0.011   0.003   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01015 ( 3582)
  covalent geometry    : angle       1.60836 ( 4794)
  hydrogen bonds       : bond        0.16174 (   92)
  hydrogen bonds       : angle       7.93774 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LYS cc_start: 0.8337 (mttt) cc_final: 0.7745 (pttt)
REVERT: B  340 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8153 (mttt)
REVERT: B  342 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7090 (mp0)
REVERT: B  343 LYS cc_start: 0.8341 (mttt) cc_final: 0.7935 (mtpt)
REVERT: C  343 LYS cc_start: 0.8212 (mttt) cc_final: 0.7972 (mtpt)
REVERT: C  375 LYS cc_start: 0.8166 (tttt) cc_final: 0.7320 (ttmm)
REVERT: D  338 GLU cc_start: 0.8457 (tt0) cc_final: 0.8228 (tt0)
REVERT: D  343 LYS cc_start: 0.8247 (mttt) cc_final: 0.7924 (mtpm)
REVERT: D  379 ARG cc_start: 0.6120 (mtt180) cc_final: 0.5750 (mmm160)
REVERT: E  343 LYS cc_start: 0.8149 (mttt) cc_final: 0.7803 (mtpp)
REVERT: F  340 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8003 (ttmm)
REVERT: F  343 LYS cc_start: 0.8199 (mttt) cc_final: 0.7610 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 1.3952
  time to fit residues: 205.9307
Evaluate side-chains
  95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
F 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.169252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.133746 restraints weight = 10987.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 1.76
r_work: 0.3816 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3582  Z= 0.117
  Angle     :  0.579   3.622   4794  Z= 0.301
  Chirality :  0.050   0.128    534
  Planarity :  0.004   0.032    618
  Dihedral  :  6.168  18.831    480
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.18 %
    Favored  : 85.57 %
  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: -2.27 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 349 
 TYR   0.010   0.002   TYR D 310 
 PHE   0.010   0.002   PHE A 378 
 HIS   0.005   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3582)
  covalent geometry    : angle       0.57928 ( 4794)
  hydrogen bonds       : bond        0.03058 (   92)
  hydrogen bonds       : angle       5.24345 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8518 (tt0) cc_final: 0.8295 (tt0)
REVERT: A  340 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8166 (tmtm)
REVERT: A  342 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7979 (mm-30)
REVERT: B  311 LYS cc_start: 0.8408 (mttt) cc_final: 0.7757 (pttt)
REVERT: B  340 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8280 (mttt)
REVERT: B  342 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7130 (mp0)
REVERT: B  343 LYS cc_start: 0.8600 (mttt) cc_final: 0.8148 (mtpt)
REVERT: C  340 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7934 (mttt)
REVERT: C  342 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7722 (mt-10)
REVERT: C  375 LYS cc_start: 0.7952 (tttt) cc_final: 0.7067 (ttmm)
REVERT: D  340 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7670 (mmtm)
REVERT: D  343 LYS cc_start: 0.8454 (mttt) cc_final: 0.8147 (mtpm)
REVERT: E  340 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7605 (ttpp)
REVERT: E  343 LYS cc_start: 0.8336 (mttt) cc_final: 0.7995 (mtpp)
REVERT: F  311 LYS cc_start: 0.8370 (mttt) cc_final: 0.7663 (mttm)
REVERT: F  343 LYS cc_start: 0.8415 (mttt) cc_final: 0.7741 (tptt)
REVERT: F  372 GLU cc_start: 0.8623 (tt0) cc_final: 0.8413 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 1.6243
  time to fit residues: 170.9702
Evaluate side-chains
  89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
C 368 ASN
D 368 ASN
E 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.162042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.125901 restraints weight = 11021.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 1.76
r_work: 0.3733 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3582  Z= 0.143
  Angle     :  0.554   4.112   4794  Z= 0.286
  Chirality :  0.050   0.131    534
  Planarity :  0.004   0.040    618
  Dihedral  :  5.803  16.841    480
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.41 %
    Favored  : 80.85 %
  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: -2.31 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.011   0.002   TYR C 310 
 PHE   0.009   0.001   PHE D 378 
 HIS   0.005   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3582)
  covalent geometry    : angle       0.55423 ( 4794)
  hydrogen bonds       : bond        0.02437 (   92)
  hydrogen bonds       : angle       4.63842 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8096 (mm-30)
REVERT: B  314 ASP cc_start: 0.8805 (t0) cc_final: 0.8526 (t0)
REVERT: B  338 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8333 (tm-30)
REVERT: B  340 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8294 (mttt)
REVERT: B  342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7278 (mp0)
REVERT: B  343 LYS cc_start: 0.8617 (mttt) cc_final: 0.8138 (mtpt)
REVERT: B  375 LYS cc_start: 0.8497 (tttt) cc_final: 0.7783 (ttmm)
REVERT: C  340 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8057 (mttt)
REVERT: C  342 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7762 (mt-10)
REVERT: D  340 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7593 (mmtm)
REVERT: D  343 LYS cc_start: 0.8438 (mttt) cc_final: 0.8138 (mtpm)
REVERT: E  340 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7581 (ttpp)
REVERT: E  343 LYS cc_start: 0.8353 (mttt) cc_final: 0.8012 (mtpp)
REVERT: F  311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7639 (mttm)
REVERT: F  343 LYS cc_start: 0.8388 (mttt) cc_final: 0.7688 (tptt)
  outliers start: 7
  outliers final: 3
  residues processed: 93
  average time/residue: 1.5857
  time to fit residues: 150.7687
Evaluate side-chains
  94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0670
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.165287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.129656 restraints weight = 10986.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.80
r_work: 0.3792 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3582  Z= 0.094
  Angle     :  0.479   3.330   4794  Z= 0.247
  Chirality :  0.049   0.126    534
  Planarity :  0.004   0.040    618
  Dihedral  :  5.148  13.975    480
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 17.66 %
    Favored  : 80.85 %
  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: -2.25 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.008   0.002   TYR C 310 
 PHE   0.008   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3582)
  covalent geometry    : angle       0.47853 ( 4794)
  hydrogen bonds       : bond        0.01853 (   92)
  hydrogen bonds       : angle       4.42034 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: A  369 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8726 (ttmm)
REVERT: B  311 LYS cc_start: 0.8413 (mttt) cc_final: 0.7796 (pttt)
REVERT: B  314 ASP cc_start: 0.8802 (t0) cc_final: 0.8533 (t0)
REVERT: B  338 GLU cc_start: 0.8562 (tt0) cc_final: 0.8341 (tm-30)
REVERT: B  340 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8314 (mttt)
REVERT: B  342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7326 (mp0)
REVERT: B  343 LYS cc_start: 0.8644 (mttt) cc_final: 0.8205 (mtpt)
REVERT: B  375 LYS cc_start: 0.8490 (tttt) cc_final: 0.7807 (ttmm)
REVERT: C  340 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8092 (mttt)
REVERT: C  342 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7803 (mt-10)
REVERT: D  340 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7993 (mttt)
REVERT: D  343 LYS cc_start: 0.8447 (mttt) cc_final: 0.8157 (mtpm)
REVERT: E  340 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7588 (ttpp)
REVERT: E  343 LYS cc_start: 0.8368 (mttt) cc_final: 0.8019 (mtpp)
REVERT: F  311 LYS cc_start: 0.8372 (mttt) cc_final: 0.7643 (mttm)
REVERT: F  343 LYS cc_start: 0.8419 (mttt) cc_final: 0.7752 (tptt)
  outliers start: 6
  outliers final: 4
  residues processed: 97
  average time/residue: 1.5855
  time to fit residues: 157.2823
Evaluate side-chains
  97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.165131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.130150 restraints weight = 10949.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.76
r_work: 0.3789 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.4647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3582  Z= 0.092
  Angle     :  0.468   3.327   4794  Z= 0.242
  Chirality :  0.049   0.125    534
  Planarity :  0.004   0.039    618
  Dihedral  :  4.893  13.446    480
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.41 %
    Favored  : 80.85 %
  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: -2.21 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 379 
 TYR   0.008   0.002   TYR C 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 3582)
  covalent geometry    : angle       0.46792 ( 4794)
  hydrogen bonds       : bond        0.01782 (   92)
  hydrogen bonds       : angle       4.32000 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (tm-30)
REVERT: A  340 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8182 (tmtm)
REVERT: A  342 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: B  311 LYS cc_start: 0.8389 (mttt) cc_final: 0.7798 (pttt)
REVERT: B  338 GLU cc_start: 0.8514 (tt0) cc_final: 0.8307 (tm-30)
REVERT: B  340 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8294 (mttt)
REVERT: B  342 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7376 (mp0)
REVERT: B  343 LYS cc_start: 0.8603 (mttt) cc_final: 0.8172 (mtpt)
REVERT: B  375 LYS cc_start: 0.8539 (tttt) cc_final: 0.7852 (ttmm)
REVERT: C  340 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8058 (mttt)
REVERT: D  340 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7990 (mttt)
REVERT: D  343 LYS cc_start: 0.8449 (mttt) cc_final: 0.8014 (mtpp)
REVERT: E  340 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7612 (ttpp)
REVERT: E  343 LYS cc_start: 0.8370 (mttt) cc_final: 0.7859 (mtpp)
REVERT: F  311 LYS cc_start: 0.8396 (mttt) cc_final: 0.7634 (mttm)
REVERT: F  343 LYS cc_start: 0.8433 (mttt) cc_final: 0.7758 (tptt)
  outliers start: 7
  outliers final: 3
  residues processed: 96
  average time/residue: 1.6287
  time to fit residues: 159.8454
Evaluate side-chains
  92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain E residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.166446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.131691 restraints weight = 10974.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.76
r_work: 0.3801 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3582  Z= 0.087
  Angle     :  0.456   3.688   4794  Z= 0.236
  Chirality :  0.049   0.122    534
  Planarity :  0.004   0.038    618
  Dihedral  :  4.714  13.122    480
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.41 %
    Favored  : 80.35 %
  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: -2.18 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.007   0.002   TYR C 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 3582)
  covalent geometry    : angle       0.45650 ( 4794)
  hydrogen bonds       : bond        0.01671 (   92)
  hydrogen bonds       : angle       4.21224 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8525 (tt0) cc_final: 0.8254 (tm-30)
REVERT: A  340 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8178 (tmtm)
REVERT: A  342 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8036 (mm-30)
REVERT: B  311 LYS cc_start: 0.8376 (mttt) cc_final: 0.7805 (pttt)
REVERT: B  314 ASP cc_start: 0.8809 (t0) cc_final: 0.8551 (t0)
REVERT: B  338 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (tm-30)
REVERT: B  340 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8286 (mttt)
REVERT: B  342 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7393 (mp0)
REVERT: B  343 LYS cc_start: 0.8602 (mttt) cc_final: 0.8170 (mtpt)
REVERT: B  375 LYS cc_start: 0.8544 (tttt) cc_final: 0.7869 (ttmm)
REVERT: C  340 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8031 (mttt)
REVERT: C  342 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7688 (mt-10)
REVERT: D  306 VAL cc_start: 0.7755 (m) cc_final: 0.7544 (p)
REVERT: D  340 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7986 (mttt)
REVERT: D  343 LYS cc_start: 0.8439 (mttt) cc_final: 0.8010 (mtpp)
REVERT: E  340 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7596 (ttpp)
REVERT: E  343 LYS cc_start: 0.8388 (mttt) cc_final: 0.8023 (mtpp)
REVERT: E  379 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7241 (mmm160)
REVERT: F  311 LYS cc_start: 0.8393 (mttt) cc_final: 0.7632 (mttm)
REVERT: F  343 LYS cc_start: 0.8459 (mttt) cc_final: 0.7774 (tptt)
  outliers start: 9
  outliers final: 2
  residues processed: 92
  average time/residue: 1.6166
  time to fit residues: 152.0305
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 0 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.164981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.130248 restraints weight = 10887.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.76
r_work: 0.3795 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3582  Z= 0.089
  Angle     :  0.449   3.103   4794  Z= 0.232
  Chirality :  0.049   0.124    534
  Planarity :  0.004   0.038    618
  Dihedral  :  4.629  13.172    480
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.41 %
    Favored  : 80.10 %
  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: -2.14 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.008   0.002   TYR C 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 3582)
  covalent geometry    : angle       0.44918 ( 4794)
  hydrogen bonds       : bond        0.01674 (   92)
  hydrogen bonds       : angle       4.14978 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (tm-30)
REVERT: A  340 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8184 (tmtm)
REVERT: B  311 LYS cc_start: 0.8361 (mttt) cc_final: 0.7806 (pttt)
REVERT: B  314 ASP cc_start: 0.8796 (t0) cc_final: 0.8538 (t0)
REVERT: B  340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8285 (mttt)
REVERT: B  342 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7363 (mp0)
REVERT: B  343 LYS cc_start: 0.8552 (mttt) cc_final: 0.8135 (mtpt)
REVERT: B  375 LYS cc_start: 0.8564 (tttt) cc_final: 0.7896 (ttmm)
REVERT: C  340 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8044 (mttt)
REVERT: C  375 LYS cc_start: 0.8231 (tttt) cc_final: 0.7421 (ttmm)
REVERT: D  340 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8008 (mttt)
REVERT: D  343 LYS cc_start: 0.8444 (mttt) cc_final: 0.8127 (mtpm)
REVERT: E  340 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7655 (ttpp)
REVERT: E  343 LYS cc_start: 0.8416 (mttt) cc_final: 0.8048 (mtpp)
REVERT: E  369 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8501 (ttmt)
REVERT: F  311 LYS cc_start: 0.8365 (mttt) cc_final: 0.7606 (mttm)
REVERT: F  343 LYS cc_start: 0.8471 (mttt) cc_final: 0.7782 (tptt)
  outliers start: 6
  outliers final: 3
  residues processed: 91
  average time/residue: 1.6590
  time to fit residues: 154.2640
Evaluate side-chains
  90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C 327 ASN
D 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.162691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.127926 restraints weight = 11038.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 1.76
r_work: 0.3776 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.4936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3582  Z= 0.100
  Angle     :  0.465   3.961   4794  Z= 0.240
  Chirality :  0.049   0.125    534
  Planarity :  0.004   0.039    618
  Dihedral  :  4.723  13.456    480
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.91 %
    Favored  : 79.10 %
  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: -2.14 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.008   0.002   TYR D 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3582)
  covalent geometry    : angle       0.46463 ( 4794)
  hydrogen bonds       : bond        0.01734 (   92)
  hydrogen bonds       : angle       4.12909 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7815 (m-40)
REVERT: A  338 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8292 (tm-30)
REVERT: B  311 LYS cc_start: 0.8370 (mttt) cc_final: 0.7842 (pttt)
REVERT: B  314 ASP cc_start: 0.8800 (t0) cc_final: 0.8547 (t0)
REVERT: B  340 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8289 (mttt)
REVERT: B  342 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7395 (mp0)
REVERT: B  343 LYS cc_start: 0.8565 (mttt) cc_final: 0.8161 (mtpt)
REVERT: B  375 LYS cc_start: 0.8587 (tttt) cc_final: 0.7931 (ttmm)
REVERT: C  306 VAL cc_start: 0.7714 (m) cc_final: 0.7485 (p)
REVERT: C  340 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8066 (mttt)
REVERT: C  375 LYS cc_start: 0.8222 (tttt) cc_final: 0.7442 (ttmm)
REVERT: D  340 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8000 (mttt)
REVERT: D  343 LYS cc_start: 0.8488 (mttt) cc_final: 0.8182 (mtpm)
REVERT: E  340 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7661 (ttpp)
REVERT: E  343 LYS cc_start: 0.8461 (mttt) cc_final: 0.8093 (mtpp)
REVERT: E  369 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8501 (ttmt)
REVERT: F  311 LYS cc_start: 0.8400 (mttt) cc_final: 0.7634 (mttm)
REVERT: F  343 LYS cc_start: 0.8492 (mttt) cc_final: 0.7829 (tptt)
  outliers start: 8
  outliers final: 2
  residues processed: 89
  average time/residue: 1.6835
  time to fit residues: 153.1175
Evaluate side-chains
  88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 327 ASN
D 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.164449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.130181 restraints weight = 11041.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 1.75
r_work: 0.3796 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3582  Z= 0.094
  Angle     :  0.458   3.118   4794  Z= 0.237
  Chirality :  0.049   0.124    534
  Planarity :  0.004   0.039    618
  Dihedral  :  4.642  13.392    480
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 19.90 %
    Favored  : 78.86 %
  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: -2.11 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 349 
 TYR   0.007   0.002   TYR D 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 3582)
  covalent geometry    : angle       0.45755 ( 4794)
  hydrogen bonds       : bond        0.01687 (   92)
  hydrogen bonds       : angle       4.09448 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7711 (m-40)
REVERT: A  338 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8282 (tm-30)
REVERT: B  311 LYS cc_start: 0.8375 (mttt) cc_final: 0.7867 (pttt)
REVERT: B  340 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8277 (mttt)
REVERT: B  342 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7411 (mp0)
REVERT: B  343 LYS cc_start: 0.8580 (mttt) cc_final: 0.8176 (mtpt)
REVERT: B  375 LYS cc_start: 0.8584 (tttt) cc_final: 0.7936 (ttmm)
REVERT: C  340 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8069 (mttt)
REVERT: C  375 LYS cc_start: 0.8248 (tttt) cc_final: 0.7482 (ttmm)
REVERT: D  340 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8008 (mttt)
REVERT: D  343 LYS cc_start: 0.8504 (mttt) cc_final: 0.8198 (mtpm)
REVERT: E  340 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7680 (ttpp)
REVERT: E  343 LYS cc_start: 0.8466 (mttt) cc_final: 0.8097 (mtpp)
REVERT: E  349 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7838 (mtm180)
REVERT: E  369 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8502 (ttmt)
REVERT: F  311 LYS cc_start: 0.8397 (mttt) cc_final: 0.7638 (mttm)
REVERT: F  343 LYS cc_start: 0.8485 (mttt) cc_final: 0.7818 (tptt)
  outliers start: 5
  outliers final: 1
  residues processed: 89
  average time/residue: 1.6685
  time to fit residues: 151.6603
Evaluate side-chains
  86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0670
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
D 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.166085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.132041 restraints weight = 11010.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.75
r_work: 0.3821 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3582  Z= 0.079
  Angle     :  0.444   3.228   4794  Z= 0.230
  Chirality :  0.049   0.126    534
  Planarity :  0.004   0.038    618
  Dihedral  :  4.375  13.068    480
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 20.40 %
    Favored  : 78.86 %
  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: -2.11 (0.33), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.006   0.001   TYR D 310 
 PHE   0.005   0.001   PHE D 378 
 HIS   0.003   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 3582)
  covalent geometry    : angle       0.44413 ( 4794)
  hydrogen bonds       : bond        0.01585 (   92)
  hydrogen bonds       : angle       3.99026 (  276)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8261 (tm-30)
REVERT: B  311 LYS cc_start: 0.8333 (mttt) cc_final: 0.7844 (pttt)
REVERT: B  314 ASP cc_start: 0.8821 (t0) cc_final: 0.8604 (t0)
REVERT: B  340 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8270 (mttt)
REVERT: B  342 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7392 (mp0)
REVERT: B  343 LYS cc_start: 0.8571 (mttt) cc_final: 0.8164 (mtpt)
REVERT: B  375 LYS cc_start: 0.8581 (tttt) cc_final: 0.7924 (ttmm)
REVERT: C  340 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8048 (mttt)
REVERT: D  340 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7997 (mttt)
REVERT: D  343 LYS cc_start: 0.8482 (mttt) cc_final: 0.8168 (mtpm)
REVERT: E  340 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7635 (ttpp)
REVERT: E  343 LYS cc_start: 0.8457 (mttt) cc_final: 0.8092 (mtpp)
REVERT: E  349 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7768 (mtm180)
REVERT: E  369 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8463 (ttmt)
REVERT: E  379 ARG cc_start: 0.7357 (mmm160) cc_final: 0.6322 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8367 (mttt) cc_final: 0.7605 (mttm)
REVERT: F  343 LYS cc_start: 0.8460 (mttt) cc_final: 0.7804 (tptt)
  outliers start: 3
  outliers final: 1
  residues processed: 89
  average time/residue: 1.6424
  time to fit residues: 149.1174
Evaluate side-chains
  88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain F residue  341 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0470
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.2084

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.162276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.127372 restraints weight = 10908.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 1.76
r_work: 0.3750 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3655 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3582  Z= 0.118
  Angle     :  0.473   3.172   4794  Z= 0.246
  Chirality :  0.049   0.122    534
  Planarity :  0.004   0.039    618
  Dihedral  :  4.811  14.281    480
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 21.39 %
    Favored  : 77.86 %
  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: -2.11 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.009   0.002   TYR D 310 
 PHE   0.007   0.001   PHE D 378 
 HIS   0.004   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3582)
  covalent geometry    : angle       0.47299 ( 4794)
  hydrogen bonds       : bond        0.01809 (   92)
  hydrogen bonds       : angle       4.04816 (  276)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4295.16 seconds
wall clock time: 73 minutes 30.35 seconds (4410.35 seconds total)