Starting phenix.real_space_refine
on Fri Aug 22 13:46:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zx6_60539/08_2025/8zx6_60539.cif"
  }
  resolution = 3.5
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2172      2.51       5
     N     642      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3468
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 0.74, per 1000 atoms: 0.21
  Number of scatterers: 3468
  At special positions: 0
  Unit cell: (155.21, 83.83, 34.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     648      8.00
     N     642      7.00
     C    2172      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 143.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.678A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.879A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.830A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322
      removed outlier: 6.356A  pdb=" N   LYS A 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.236A  pdb=" N   ASP A 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354
      removed outlier: 6.722A  pdb=" N   LYS A 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LYS B 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.812A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377
    Processing sheet with id=AB2, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.669A  pdb=" N   GLN C 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   TYR E 310 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL C 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   GLN E 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   TYR F 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL E 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.871A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.824A  pdb=" N   LYS C 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LYS E 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 321 through 322
      removed outlier: 6.352A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LYS E 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 338
    Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.229A  pdb=" N   ASP C 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP E 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'C' and resid 353 through 354
      removed outlier: 6.720A  pdb=" N   LYS C 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LYS E 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362
    Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371
      removed outlier: 6.806A  pdb=" N   LYS C 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LYS E 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 377

    28 hydrogen bonds defined for protein.
    84 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: 0.46

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1146
        1.34 -     1.46: 573
        1.46 -     1.57: 1797
        1.57 -     1.69: 0
        1.69 -     1.80: 6
  Bond restraints: 3522
  Sorted by residual:
  bond pdb=" N   LYS B 370 "
       pdb=" CA  LYS B 370 "
    ideal  model  delta    sigma   weight residual
    1.464  1.452  0.011 1.25e-02 6.40e+03 8.04e-01
  bond pdb=" CA  LYS E 370 "
       pdb=" C   LYS E 370 "
    ideal  model  delta    sigma   weight residual
    1.526  1.516  0.009 1.08e-02 8.57e+03 7.70e-01
  bond pdb=" N   LYS A 370 "
       pdb=" CA  LYS A 370 "
    ideal  model  delta    sigma   weight residual
    1.464  1.453  0.011 1.25e-02 6.40e+03 7.58e-01
  bond pdb=" N   LYS E 370 "
       pdb=" CA  LYS E 370 "
    ideal  model  delta    sigma   weight residual
    1.464  1.453  0.011 1.25e-02 6.40e+03 7.52e-01
  bond pdb=" CA  LYS F 370 "
       pdb=" C   LYS F 370 "
    ideal  model  delta    sigma   weight residual
    1.526  1.516  0.009 1.08e-02 8.57e+03 7.35e-01
  ... (remaining 3517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4230
        1.06 -     2.12: 376
        2.12 -     3.19: 60
        3.19 -     4.25: 29
        4.25 -     5.31: 15
  Bond angle restraints: 4710
  Sorted by residual:
  angle pdb=" C   ASP E 348 "
        pdb=" N   ARG E 349 "
        pdb=" CA  ARG E 349 "
      ideal   model   delta    sigma   weight residual
     122.61  125.95   -3.34 1.56e+00 4.11e-01 4.59e+00
  angle pdb=" C   ASP C 348 "
        pdb=" N   ARG C 349 "
        pdb=" CA  ARG C 349 "
      ideal   model   delta    sigma   weight residual
     122.61  125.94   -3.33 1.56e+00 4.11e-01 4.55e+00
  angle pdb=" C   ASP F 348 "
        pdb=" N   ARG F 349 "
        pdb=" CA  ARG F 349 "
      ideal   model   delta    sigma   weight residual
     122.61  125.93   -3.32 1.56e+00 4.11e-01 4.54e+00
  angle pdb=" C   ASP D 348 "
        pdb=" N   ARG D 349 "
        pdb=" CA  ARG D 349 "
      ideal   model   delta    sigma   weight residual
     122.61  125.91   -3.30 1.56e+00 4.11e-01 4.46e+00
  angle pdb=" C   ASP A 348 "
        pdb=" N   ARG A 349 "
        pdb=" CA  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     122.61  125.89   -3.28 1.56e+00 4.11e-01 4.42e+00
  ... (remaining 4705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.10: 1932
       15.10 -    30.20: 174
       30.20 -    45.30: 30
       45.30 -    60.40: 0
       60.40 -    75.50: 6
  Dihedral angle restraints: 2142
    sinusoidal: 894
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  ASP E 358 "
           pdb=" C   ASP E 358 "
           pdb=" N   ASN E 359 "
           pdb=" CA  ASN E 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.31   14.69     0      5.00e+00 4.00e-02 8.63e+00
  dihedral pdb=" CA  ASP D 358 "
           pdb=" C   ASP D 358 "
           pdb=" N   ASN D 359 "
           pdb=" CA  ASN D 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.32   14.68     0      5.00e+00 4.00e-02 8.62e+00
  dihedral pdb=" CA  ASP F 358 "
           pdb=" C   ASP F 358 "
           pdb=" N   ASN F 359 "
           pdb=" CA  ASN F 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.35   14.65     0      5.00e+00 4.00e-02 8.59e+00
  ... (remaining 2139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 258
       0.026 -    0.051: 136
       0.051 -    0.077: 35
       0.077 -    0.102: 36
       0.102 -    0.128: 63
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  VAL B 339 "
            pdb=" N   VAL B 339 "
            pdb=" C   VAL B 339 "
            pdb=" CB  VAL B 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE B 371 "
            pdb=" N   ILE B 371 "
            pdb=" C   ILE B 371 "
            pdb=" CB  ILE B 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  VAL D 339 "
            pdb=" N   VAL D 339 "
            pdb=" C   VAL D 339 "
            pdb=" CB  VAL D 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 525 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.008 2.00e-02 2.50e+03   5.82e-03 6.78e-01
        pdb=" CG  TYR E 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.008 2.00e-02 2.50e+03   5.69e-03 6.48e-01
        pdb=" CG  TYR F 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.008 2.00e-02 2.50e+03   5.68e-03 6.44e-01
        pdb=" CG  TYR C 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.001 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1075
        2.85 -     3.36: 2650
        3.36 -     3.88: 5547
        3.88 -     4.39: 5314
        4.39 -     4.90: 11791
  Nonbonded interactions: 26377
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 338 "
            pdb=" NZ  LYS B 331 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OE1 GLU E 338 "
            pdb=" NZ  LYS D 331 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OE1 GLU A 338 "
            pdb=" NZ  LYS C 331 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OE1 GLU B 338 "
            pdb=" NZ  LYS E 331 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OE1 GLU D 338 "
            pdb=" NZ  LYS F 331 "
     model   vdw
     2.345 3.120
  ... (remaining 26372 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.380
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3522  Z= 0.226
  Angle     :  0.769   5.310   4710  Z= 0.429
  Chirality :  0.052   0.128    528
  Planarity :  0.002   0.014    600
  Dihedral  : 12.489  75.495   1350
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  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: -4.38 (0.26), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.20), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.014   0.003   TYR E 310 
 PHE   0.005   0.001   PHE E 378 
 HIS   0.003   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 3522)
  covalent geometry    : angle       0.76886 ( 4710)
  hydrogen bonds       : bond        0.13574 (   28)
  hydrogen bonds       : angle       5.44003 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.144 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7409 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.2358
  time to fit residues: 7.9599
Evaluate side-chains
  23 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.6586

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.120671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.102502 restraints weight = 4833.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.104910 restraints weight = 2391.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.106535 restraints weight = 1581.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.107643 restraints weight = 1216.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.108340 restraints weight = 1022.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3522  Z= 0.221
  Angle     :  0.682   5.375   4710  Z= 0.345
  Chirality :  0.053   0.121    528
  Planarity :  0.003   0.025    600
  Dihedral  :  5.673  15.151    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.06 %
    Favored  : 92.93 %
  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: -3.86 (0.29), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.22), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.026   0.006   TYR C 310 
 PHE   0.005   0.001   PHE F 378 
 HIS   0.005   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 3522)
  covalent geometry    : angle       0.68235 ( 4710)
  hydrogen bonds       : bond        0.02804 (   28)
  hydrogen bonds       : angle       3.67016 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.152 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8753 (mt) cc_final: 0.8487 (mp)
REVERT: D  342 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7534 (pm20)
REVERT: D  375 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7075 (tmtt)
REVERT: F  325 LEU cc_start: 0.8715 (mt) cc_final: 0.8449 (mp)
REVERT: F  342 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7608 (pm20)
REVERT: F  375 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7402 (mtpp)
  outliers start: 4
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1624
  time to fit residues: 5.0881
Evaluate side-chains
  27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0870
   chunk 22 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    3.3964

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.120466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.101642 restraints weight = 4782.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.104320 restraints weight = 2219.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.106053 restraints weight = 1431.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.107288 restraints weight = 1092.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.108006 restraints weight = 908.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3522  Z= 0.200
  Angle     :  0.648   4.849   4710  Z= 0.331
  Chirality :  0.052   0.120    528
  Planarity :  0.003   0.025    600
  Dihedral  :  5.407  14.203    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.57 %
    Favored  : 91.92 %
  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: -3.69 (0.30), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 379 
 TYR   0.024   0.006   TYR C 310 
 PHE   0.006   0.002   PHE F 378 
 HIS   0.005   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3522)
  covalent geometry    : angle       0.64775 ( 4710)
  hydrogen bonds       : bond        0.02128 (   28)
  hydrogen bonds       : angle       3.26368 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.148 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8740 (mt) cc_final: 0.8518 (mp)
REVERT: D  342 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7554 (pm20)
REVERT: D  375 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7076 (tmtt)
REVERT: F  325 LEU cc_start: 0.8671 (mt) cc_final: 0.8444 (mp)
REVERT: F  342 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7537 (pm20)
REVERT: F  375 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7422 (mtpp)
  outliers start: 6
  outliers final: 5
  residues processed: 32
  average time/residue: 0.1538
  time to fit residues: 5.5126
Evaluate side-chains
  27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   overall best weight:    3.8786

-------------------------------------------------------------------------------
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 = 0.4233 r_free = 0.4233 target = 0.119459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.100890 restraints weight = 4756.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.103416 restraints weight = 2301.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.105145 restraints weight = 1516.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.106204 restraints weight = 1167.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.106984 restraints weight = 986.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3522  Z= 0.223
  Angle     :  0.662   5.042   4710  Z= 0.342
  Chirality :  0.053   0.120    528
  Planarity :  0.003   0.028    600
  Dihedral  :  5.431  14.820    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  7.32 %
    Favored  : 90.91 %
  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: -3.61 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 379 
 TYR   0.024   0.006   TYR A 310 
 PHE   0.008   0.002   PHE D 378 
 HIS   0.005   0.001   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 3522)
  covalent geometry    : angle       0.66222 ( 4710)
  hydrogen bonds       : bond        0.02017 (   28)
  hydrogen bonds       : angle       3.16946 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.134 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7445 (pm20)
REVERT: D  375 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7124 (tmtt)
REVERT: F  325 LEU cc_start: 0.8668 (mt) cc_final: 0.8460 (mp)
REVERT: F  342 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7545 (pm20)
REVERT: F  375 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7013 (tmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 32
  average time/residue: 0.1532
  time to fit residues: 5.4777
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.115176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.096749 restraints weight = 4975.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.099267 restraints weight = 2371.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.100868 restraints weight = 1549.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.101981 restraints weight = 1195.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.102633 restraints weight = 1008.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3522  Z= 0.326
  Angle     :  0.773   5.577   4710  Z= 0.407
  Chirality :  0.056   0.127    528
  Planarity :  0.004   0.028    600
  Dihedral  :  5.852  15.181    468
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.35 %
    Favored  : 87.63 %
  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: -3.78 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.030   0.008   TYR D 310 
 PHE   0.011   0.003   PHE F 378 
 HIS   0.008   0.002   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 ( 3522)
  covalent geometry    : angle       0.77272 ( 4710)
  hydrogen bonds       : bond        0.02403 (   28)
  hydrogen bonds       : angle       3.29292 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C  328 ILE cc_start: 0.9170 (mt) cc_final: 0.8846 (mp)
REVERT: B  328 ILE cc_start: 0.8940 (mt) cc_final: 0.8676 (mp)
REVERT: B  378 PHE cc_start: 0.8400 (t80) cc_final: 0.8120 (t80)
REVERT: D  342 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7482 (pm20)
REVERT: D  375 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7116 (tmtt)
REVERT: F  325 LEU cc_start: 0.8666 (mt) cc_final: 0.8448 (mp)
REVERT: F  342 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7637 (pm20)
REVERT: F  375 LYS cc_start: 0.7984 (ttmt) cc_final: 0.6980 (tttm)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1338
  time to fit residues: 5.2769
Evaluate side-chains
  35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.4297 r_free = 0.4297 target = 0.123429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.104206 restraints weight = 4606.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.106901 restraints weight = 2250.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.108669 restraints weight = 1483.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.109750 restraints weight = 1139.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.110563 restraints weight = 963.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   3522  Z= 0.124
  Angle     :  0.594   5.221   4710  Z= 0.301
  Chirality :  0.051   0.122    528
  Planarity :  0.003   0.025    600
  Dihedral  :  5.027  13.693    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.09 %
    Favored  : 89.14 %
  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: -3.44 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.004   0.001   PHE F 378 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3522)
  covalent geometry    : angle       0.59434 ( 4710)
  hydrogen bonds       : bond        0.01193 (   28)
  hydrogen bonds       : angle       3.21289 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.145 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7372 (pm20)
REVERT: D  375 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7051 (tmtt)
REVERT: F  342 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7527 (pm20)
REVERT: F  375 LYS cc_start: 0.7919 (ttmt) cc_final: 0.6991 (tmtt)
  outliers start: 7
  outliers final: 2
  residues processed: 36
  average time/residue: 0.1386
  time to fit residues: 5.6530
Evaluate side-chains
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.119765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.101116 restraints weight = 4816.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.103478 restraints weight = 2501.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.105049 restraints weight = 1686.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.106011 restraints weight = 1309.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.106742 restraints weight = 1115.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3522  Z= 0.229
  Angle     :  0.695   5.525   4710  Z= 0.357
  Chirality :  0.053   0.125    528
  Planarity :  0.004   0.025    600
  Dihedral  :  5.387  14.601    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.61 %
    Favored  : 87.63 %
  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: -3.57 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.023   0.006   TYR C 310 
 PHE   0.009   0.002   PHE D 378 
 HIS   0.006   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 3522)
  covalent geometry    : angle       0.69485 ( 4710)
  hydrogen bonds       : bond        0.01828 (   28)
  hydrogen bonds       : angle       3.27439 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.123 
Fit side-chains
REVERT: C  328 ILE cc_start: 0.9175 (mt) cc_final: 0.8860 (mp)
REVERT: B  378 PHE cc_start: 0.8332 (t80) cc_final: 0.8120 (t80)
REVERT: D  342 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7509 (pm20)
REVERT: F  342 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7666 (pm20)
REVERT: F  375 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7040 (tmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 28
  average time/residue: 0.1275
  time to fit residues: 4.0107
Evaluate side-chains
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    3.6588

-------------------------------------------------------------------------------
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 = 0.4240 r_free = 0.4240 target = 0.119214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.100344 restraints weight = 4838.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.102862 restraints weight = 2361.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.104571 restraints weight = 1566.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.105587 restraints weight = 1208.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.106350 restraints weight = 1028.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3522  Z= 0.211
  Angle     :  0.679   5.762   4710  Z= 0.348
  Chirality :  0.053   0.127    528
  Planarity :  0.003   0.023    600
  Dihedral  :  5.415  14.512    468
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.87 %
    Favored  : 86.36 %
  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: -3.56 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.021   0.005   TYR C 310 
 PHE   0.008   0.002   PHE F 378 
 HIS   0.005   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3522)
  covalent geometry    : angle       0.67915 ( 4710)
  hydrogen bonds       : bond        0.01691 (   28)
  hydrogen bonds       : angle       3.33670 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.139 
Fit side-chains
REVERT: B  378 PHE cc_start: 0.8316 (t80) cc_final: 0.8059 (t80)
REVERT: D  342 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7419 (pm20)
REVERT: F  342 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7556 (pm20)
REVERT: F  375 LYS cc_start: 0.7931 (ttmt) cc_final: 0.6985 (tmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 28
  average time/residue: 0.1659
  time to fit residues: 5.2385
Evaluate side-chains
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    2.8784

-------------------------------------------------------------------------------
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 = 0.4262 r_free = 0.4262 target = 0.120713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.101698 restraints weight = 4688.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.104278 restraints weight = 2281.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.106034 restraints weight = 1505.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.107105 restraints weight = 1157.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.107816 restraints weight = 980.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3522  Z= 0.169
  Angle     :  0.645   6.723   4710  Z= 0.329
  Chirality :  0.052   0.124    528
  Planarity :  0.003   0.022    600
  Dihedral  :  5.203  13.951    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.88 %
    Favored  : 85.10 %
  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: -3.52 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.018   0.004   TYR A 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.004   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3522)
  covalent geometry    : angle       0.64514 ( 4710)
  hydrogen bonds       : bond        0.01447 (   28)
  hydrogen bonds       : angle       3.33697 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.111 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7433 (pm20)
REVERT: F  342 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7540 (pm20)
REVERT: F  375 LYS cc_start: 0.7921 (ttmt) cc_final: 0.6975 (tmtt)
  outliers start: 8
  outliers final: 6
  residues processed: 28
  average time/residue: 0.1474
  time to fit residues: 4.7090
Evaluate side-chains
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0170
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   overall best weight:    3.3224

-------------------------------------------------------------------------------
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 = 0.4243 r_free = 0.4243 target = 0.119746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.100806 restraints weight = 4756.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.103349 restraints weight = 2323.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.105068 restraints weight = 1537.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.106132 restraints weight = 1187.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.106868 restraints weight = 1005.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3522  Z= 0.195
  Angle     :  0.676   7.702   4710  Z= 0.344
  Chirality :  0.053   0.131    528
  Planarity :  0.003   0.022    600
  Dihedral  :  5.297  14.029    468
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.37 %
    Favored  : 85.86 %
  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: -3.52 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.021   0.005   TYR C 310 
 PHE   0.008   0.002   PHE D 378 
 HIS   0.005   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 3522)
  covalent geometry    : angle       0.67623 ( 4710)
  hydrogen bonds       : bond        0.01604 (   28)
  hydrogen bonds       : angle       3.35546 (   84)

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.122 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7433 (pm20)
REVERT: F  342 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7556 (pm20)
REVERT: F  375 LYS cc_start: 0.7914 (ttmt) cc_final: 0.6984 (tmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 28
  average time/residue: 0.1460
  time to fit residues: 4.6280
Evaluate side-chains
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain F residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 6 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0970
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.6784

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.121306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.102253 restraints weight = 4711.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.104789 restraints weight = 2285.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.106599 restraints weight = 1511.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.107701 restraints weight = 1158.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.108469 restraints weight = 976.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3522  Z= 0.161
  Angle     :  0.645   7.831   4710  Z= 0.326
  Chirality :  0.052   0.126    528
  Planarity :  0.003   0.025    600
  Dihedral  :  5.136  13.950    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.63 %
    Favored  : 85.61 %
  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 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG F 349 
 TYR   0.019   0.004   TYR C 310 
 PHE   0.006   0.001   PHE D 378 
 HIS   0.004   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3522)
  covalent geometry    : angle       0.64544 ( 4710)
  hydrogen bonds       : bond        0.01374 (   28)
  hydrogen bonds       : angle       3.34838 (   84)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 746.58 seconds
wall clock time: 13 minutes 37.44 seconds (817.44 seconds total)