Starting phenix.real_space_refine
on Wed Mar  5 20:28:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zx6_60539/03_2025/8zx6_60539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zx6_60539/03_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_60539/03_2025/8zx6_60539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zx6_60539/03_2025/8zx6_60539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zx6_60539/03_2025/8zx6_60539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zx6_60539/03_2025/8zx6_60539.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.04, per 1000 atoms: 0.88
  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: 0.97
  Conformation dependent library (CDL) restraints added in 414.7 milliseconds
  

  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: 0.65
  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: 0.77

  Time building geometry restraints manager: 1.14 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: 0.04
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:             3.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.280
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.350
-------------------------------------------------------------------------------
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= 0.292
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.003   0.001   HIS C 362 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.014   0.003   TYR E 310 
 ARG   0.001   0.000   ARG B 349 

*********************** 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  : 0.430 
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: 0.4417
  time to fit residues: 15.2180
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  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0070
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.4004

-------------------------------------------------------------------------------
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 = 0.4324 r_free = 0.4324 target = 0.127185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.108179 restraints weight = 4557.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.110704 restraints weight = 2346.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.112365 restraints weight = 1575.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   3522  Z= 0.162
  Angle     :  0.564   5.547   4710  Z= 0.279
  Chirality :  0.050   0.115    528
  Planarity :  0.002   0.026    600
  Dihedral  :  5.144  13.633    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.81 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.68 (0.28), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.22), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.003   0.001   PHE E 378 
 TYR   0.013   0.003   TYR D 310 
 ARG   0.003   0.000   ARG D 379 

*********************** 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
  33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.382 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8763 (mt) cc_final: 0.8451 (mp)
REVERT: D  375 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7089 (tttp)
REVERT: F  325 LEU cc_start: 0.8742 (mt) cc_final: 0.8401 (mp)
REVERT: F  342 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7592 (pm20)
REVERT: F  375 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7322 (mtpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.4200
  time to fit residues: 15.3451
Evaluate side-chains
  26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.118066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.100318 restraints weight = 4861.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.102523 restraints weight = 2490.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.103995 restraints weight = 1679.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3522  Z= 0.456
  Angle     :  0.748   5.449   4710  Z= 0.391
  Chirality :  0.055   0.123    528
  Planarity :  0.004   0.029    600
  Dihedral  :  5.818  15.891    468
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  6.57 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.30), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS E 362 
 PHE   0.010   0.003   PHE F 378 
 TYR   0.034   0.009   TYR C 310 
 ARG   0.001   0.000   ARG E 349 

*********************** 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
  42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.391 
Fit side-chains
REVERT: C  328 ILE cc_start: 0.9185 (mt) cc_final: 0.8875 (mp)
REVERT: B  378 PHE cc_start: 0.8350 (t80) cc_final: 0.7968 (t80)
REVERT: D  325 LEU cc_start: 0.8772 (mt) cc_final: 0.8568 (mp)
REVERT: D  342 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7607 (pm20)
REVERT: D  375 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7146 (tmtt)
REVERT: F  325 LEU cc_start: 0.8699 (mt) cc_final: 0.8473 (mp)
REVERT: F  342 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7562 (pm20)
REVERT: F  375 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7028 (tttm)
  outliers start: 8
  outliers final: 5
  residues processed: 39
  average time/residue: 0.3165
  time to fit residues: 14.0103
Evaluate side-chains
  36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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 25 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.4278 r_free = 0.4278 target = 0.122701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.103671 restraints weight = 4665.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.106373 restraints weight = 2243.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.108070 restraints weight = 1465.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3522  Z= 0.233
  Angle     :  0.613   6.043   4710  Z= 0.311
  Chirality :  0.051   0.120    528
  Planarity :  0.003   0.032    600
  Dihedral  :  5.232  14.047    468
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.005   0.001   PHE F 378 
 TYR   0.018   0.004   TYR C 310 
 ARG   0.001   0.000   ARG F 379 

*********************** 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
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.430 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8737 (mt) cc_final: 0.8510 (mp)
REVERT: D  342 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7545 (pm20)
REVERT: D  375 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7104 (tmtt)
REVERT: F  325 LEU cc_start: 0.8660 (mt) cc_final: 0.8441 (mp)
REVERT: F  342 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7493 (pm20)
REVERT: F  375 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7011 (tmtt)
  outliers start: 6
  outliers final: 4
  residues processed: 29
  average time/residue: 0.3715
  time to fit residues: 12.3567
Evaluate side-chains
  26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0770
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.1142

-------------------------------------------------------------------------------
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 = 0.4358 r_free = 0.4358 target = 0.129804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.109830 restraints weight = 4442.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.112440 restraints weight = 2299.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.114254 restraints weight = 1552.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   3522  Z= 0.125
  Angle     :  0.530   7.576   4710  Z= 0.264
  Chirality :  0.049   0.115    528
  Planarity :  0.003   0.026    600
  Dihedral  :  4.615  13.067    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.58 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 362 
 PHE   0.002   0.000   PHE D 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 379 

*********************** 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
  30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.404 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8614 (mt) cc_final: 0.8399 (mp)
REVERT: D  342 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7542 (pm20)
REVERT: D  375 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7106 (tmtt)
REVERT: F  325 LEU cc_start: 0.8659 (mt) cc_final: 0.8412 (mp)
REVERT: F  342 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7488 (pm20)
REVERT: F  375 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7364 (mtpp)
  outliers start: 4
  outliers final: 1
  residues processed: 29
  average time/residue: 0.3744
  time to fit residues: 12.4813
Evaluate side-chains
  25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0020
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.3996

-------------------------------------------------------------------------------
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 = 0.4293 r_free = 0.4293 target = 0.125418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.106064 restraints weight = 4609.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.108589 restraints weight = 2333.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.110299 restraints weight = 1557.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3522  Z= 0.215
  Angle     :  0.569   4.998   4710  Z= 0.288
  Chirality :  0.050   0.117    528
  Planarity :  0.003   0.027    600
  Dihedral  :  4.802  13.242    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.07 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.005   0.001   PHE F 378 
 TYR   0.018   0.004   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

*********************** 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
  25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.442 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7443 (pm20)
REVERT: D  375 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7114 (tmtt)
REVERT: F  325 LEU cc_start: 0.8641 (mt) cc_final: 0.8435 (mp)
REVERT: F  342 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7602 (pm20)
REVERT: F  375 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7018 (tmtt)
  outliers start: 6
  outliers final: 5
  residues processed: 23
  average time/residue: 0.3767
  time to fit residues: 10.0053
Evaluate side-chains
  24 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain C 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.120508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.101487 restraints weight = 4713.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.104088 restraints weight = 2274.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.105862 restraints weight = 1495.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3522  Z= 0.292
  Angle     :  0.625   5.577   4710  Z= 0.319
  Chirality :  0.051   0.119    528
  Planarity :  0.004   0.025    600
  Dihedral  :  5.122  13.992    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.007   0.002   PHE F 378 
 TYR   0.023   0.006   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

*********************** 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
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9137 (mt) cc_final: 0.8778 (mp)
REVERT: D  342 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7445 (pm20)
REVERT: D  375 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7116 (tmtt)
REVERT: F  325 LEU cc_start: 0.8621 (mt) cc_final: 0.8402 (mp)
REVERT: F  342 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7553 (pm20)
REVERT: F  375 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7015 (tmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 26
  average time/residue: 0.3785
  time to fit residues: 11.2399
Evaluate side-chains
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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 30 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0870
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    3.6166

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.121100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.102148 restraints weight = 4725.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.104634 restraints weight = 2341.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.106219 restraints weight = 1548.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3522  Z= 0.309
  Angle     :  0.639   5.590   4710  Z= 0.330
  Chirality :  0.052   0.121    528
  Planarity :  0.004   0.024    600
  Dihedral  :  5.253  14.372    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  7.32 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 362 
 PHE   0.008   0.002   PHE F 378 
 TYR   0.025   0.006   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

*********************** 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
  33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9148 (mt) cc_final: 0.8799 (mp)
REVERT: B  378 PHE cc_start: 0.8411 (t80) cc_final: 0.8152 (t80)
REVERT: D  342 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7464 (pm20)
REVERT: D  375 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7120 (tmtt)
REVERT: F  325 LEU cc_start: 0.8623 (mt) cc_final: 0.8415 (mp)
REVERT: F  342 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7595 (pm20)
REVERT: F  375 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7032 (tmtt)
  outliers start: 9
  outliers final: 5
  residues processed: 30
  average time/residue: 0.3625
  time to fit residues: 12.6472
Evaluate side-chains
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.118213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.099630 restraints weight = 4775.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.102151 restraints weight = 2314.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.103841 restraints weight = 1528.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3522  Z= 0.358
  Angle     :  0.684   6.557   4710  Z= 0.354
  Chirality :  0.053   0.124    528
  Planarity :  0.004   0.023    600
  Dihedral  :  5.431  14.704    468
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D 362 
 PHE   0.009   0.002   PHE F 378 
 TYR   0.028   0.007   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

*********************** 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
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7571 (ptpt)
REVERT: A  328 ILE cc_start: 0.9155 (mt) cc_final: 0.8802 (mp)
REVERT: C  328 ILE cc_start: 0.9185 (mt) cc_final: 0.8871 (mp)
REVERT: B  378 PHE cc_start: 0.8303 (t80) cc_final: 0.8100 (t80)
REVERT: D  342 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7491 (pm20)
REVERT: D  375 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7104 (tmtt)
REVERT: F  325 LEU cc_start: 0.8626 (mt) cc_final: 0.8408 (mp)
REVERT: F  342 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7624 (pm20)
REVERT: F  375 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7035 (tmtt)
  outliers start: 6
  outliers final: 5
  residues processed: 32
  average time/residue: 0.3481
  time to fit residues: 12.6640
Evaluate side-chains
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.116997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.098334 restraints weight = 4914.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.100865 restraints weight = 2323.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.102512 restraints weight = 1520.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3522  Z= 0.423
  Angle     :  0.733   6.643   4710  Z= 0.385
  Chirality :  0.055   0.129    528
  Planarity :  0.004   0.030    600
  Dihedral  :  5.650  15.434    468
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.83 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D 362 
 PHE   0.010   0.003   PHE F 378 
 TYR   0.032   0.008   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

********************** 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
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7602 (ptpt)
REVERT: A  328 ILE cc_start: 0.9155 (mt) cc_final: 0.8793 (mp)
REVERT: C  328 ILE cc_start: 0.9185 (mt) cc_final: 0.8871 (mp)
REVERT: B  328 ILE cc_start: 0.8939 (mt) cc_final: 0.8678 (mp)
REVERT: B  378 PHE cc_start: 0.8352 (t80) cc_final: 0.8149 (t80)
REVERT: D  342 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7463 (pm20)
REVERT: F  325 LEU cc_start: 0.8612 (mt) cc_final: 0.8382 (mp)
REVERT: F  342 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7617 (pm20)
REVERT: F  375 LYS cc_start: 0.7935 (ttmt) cc_final: 0.6988 (tttm)
  outliers start: 6
  outliers final: 6
  residues processed: 30
  average time/residue: 0.3161
  time to fit residues: 11.0169
Evaluate side-chains
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    4.9588

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.118011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.099560 restraints weight = 4915.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.101857 restraints weight = 2528.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.103392 restraints weight = 1703.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3522  Z= 0.417
  Angle     :  0.736   5.786   4710  Z= 0.387
  Chirality :  0.055   0.134    528
  Planarity :  0.004   0.029    600
  Dihedral  :  5.702  15.544    468
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.59 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D 362 
 PHE   0.010   0.003   PHE F 378 
 TYR   0.031   0.008   TYR C 310 
 ARG   0.001   0.000   ARG B 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1422.12 seconds
wall clock time: 25 minutes 42.04 seconds (1542.04 seconds total)