Starting phenix.real_space_refine
on Mon Jan 13 18:20:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zx6_60539/01_2025/8zx6_60539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zx6_60539/01_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_60539/01_2025/8zx6_60539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zx6_60539/01_2025/8zx6_60539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zx6_60539/01_2025/8zx6_60539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zx6_60539/01_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 3.11, per 1000 atoms: 0.90
  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: 0.76
  Conformation dependent library (CDL) restraints added in 413.5 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: 0.68
  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: 0.81

  Time building geometry restraints manager: 0.89 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: 0.03
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:             1.900
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.020
  Find NCS groups from input model:        0.070
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
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  : 0.408 
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: 0.4607
  time to fit residues: 15.8055
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  : 0.403 
-------------------------------------------------------------------------------
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 = 28)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.108180 restraints weight = 4557.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.110693 restraints weight = 2346.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.112354 restraints weight = 1578.773|
|-----------------------------------------------------------------------------|
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  : 0.404 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8763 (mt) cc_final: 0.8451 (mp)
REVERT: D  375 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7088 (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: 0.7827 (ttmt) cc_final: 0.7322 (mtpp)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.4306
  time to fit residues: 15.7486
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  : 0.426 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.118364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.100519 restraints weight = 4837.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.102758 restraints weight = 2462.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.104236 restraints weight = 1659.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3522  Z= 0.424
  Angle     :  0.725   5.428   4710  Z= 0.378
  Chirality :  0.055   0.121    528
  Planarity :  0.004   0.029    600
  Dihedral  :  5.721  15.567    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  6.57 %
    Favored  : 91.67 %
  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 (0.30), 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
 HIS   0.007   0.002   HIS E 362 
 PHE   0.009   0.003   PHE F 378 
 TYR   0.033   0.008   TYR C 310 
 ARG   0.001   0.000   ARG D 379 

*********************** 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
  37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.493 
Fit side-chains
REVERT: B  378 PHE cc_start: 0.8389 (t80) cc_final: 0.8016 (t80)
REVERT: D  325 LEU cc_start: 0.8771 (mt) cc_final: 0.8542 (mp)
REVERT: D  342 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7595 (pm20)
REVERT: D  375 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7133 (tmtt)
REVERT: F  325 LEU cc_start: 0.8709 (mt) cc_final: 0.8480 (mp)
REVERT: F  342 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7524 (pm20)
REVERT: F  375 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7000 (tttm)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.3352
  time to fit residues: 13.7389
Evaluate side-chains
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.121011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.102211 restraints weight = 4727.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.104839 restraints weight = 2297.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.106565 restraints weight = 1506.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2065

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= 0.279
  Angle     :  0.638   5.774   4710  Z= 0.326
  Chirality :  0.052   0.121    528
  Planarity :  0.004   0.031    600
  Dihedral  :  5.315  14.306    468
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  6.31 %
    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: -3.58 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.23), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 362 
 PHE   0.006   0.001   PHE F 378 
 TYR   0.021   0.005   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
  32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.338 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8740 (mt) cc_final: 0.8515 (mp)
REVERT: D  342 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7551 (pm20)
REVERT: D  375 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7101 (tmtt)
REVERT: F  325 LEU cc_start: 0.8669 (mt) cc_final: 0.8443 (mp)
REVERT: F  342 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7496 (pm20)
REVERT: F  375 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7011 (tmtt)
  outliers start: 7
  outliers final: 5
  residues processed: 30
  average time/residue: 0.3585
  time to fit residues: 12.2258
Evaluate side-chains
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  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 D 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:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.123496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.104270 restraints weight = 4654.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.106726 restraints weight = 2332.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.108445 restraints weight = 1557.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3522  Z= 0.223
  Angle     :  0.597   7.556   4710  Z= 0.302
  Chirality :  0.051   0.118    528
  Planarity :  0.003   0.028    600
  Dihedral  :  5.001  13.816    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  6.06 %
    Favored  : 91.67 %
  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: -3.41 (0.31), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 362 
 PHE   0.005   0.001   PHE D 378 
 TYR   0.017   0.004   TYR D 310 
 ARG   0.001   0.000   ARG F 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
  34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 25
  time to evaluate  : 0.433 
Fit side-chains
REVERT: D  325 LEU cc_start: 0.8713 (mt) cc_final: 0.8510 (mp)
REVERT: D  342 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7471 (pm20)
REVERT: D  375 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7112 (tmtt)
REVERT: F  325 LEU cc_start: 0.8641 (mt) cc_final: 0.8428 (mp)
REVERT: F  342 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7545 (pm20)
REVERT: F  375 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7013 (tmtt)
  outliers start: 9
  outliers final: 6
  residues processed: 31
  average time/residue: 0.3676
  time to fit residues: 12.9798
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  : 0.419 
-------------------------------------------------------------------------------
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 16 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0870
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.8164

-------------------------------------------------------------------------------
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 = 0.4318 r_free = 0.4318 target = 0.126699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.107212 restraints weight = 4554.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.109689 restraints weight = 2361.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.111431 restraints weight = 1598.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   3522  Z= 0.168
  Angle     :  0.557   4.702   4710  Z= 0.280
  Chirality :  0.050   0.116    528
  Planarity :  0.003   0.026    600
  Dihedral  :  4.748  13.298    468
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.08 %
    Favored  : 91.16 %
  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: -3.28 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.004   0.001   PHE F 378 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

*********************** 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: 3
    poor density    : 22
  time to evaluate  : 0.395 
Fit side-chains
REVERT: D  342 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7397 (pm20)
REVERT: D  375 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7132 (tmtt)
REVERT: F  325 LEU cc_start: 0.8652 (mt) cc_final: 0.8441 (mp)
REVERT: F  342 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7482 (pm20)
REVERT: F  375 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7390 (mtpp)
  outliers start: 3
  outliers final: 2
  residues processed: 24
  average time/residue: 0.3504
  time to fit residues: 9.7560
Evaluate side-chains
  24 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E 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 19 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 = 0.120357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.101417 restraints weight = 4715.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.103995 restraints weight = 2278.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.105739 restraints weight = 1504.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2360

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= 0.303
  Angle     :  0.637   5.852   4710  Z= 0.326
  Chirality :  0.052   0.120    528
  Planarity :  0.004   0.026    600
  Dihedral  :  5.118  14.004    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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: -3.35 (0.32), residues: 444
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.24), 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 E 379 

*********************** 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
  27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9138 (mt) cc_final: 0.8778 (mp)
REVERT: D  342 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7494 (pm20)
REVERT: D  375 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7117 (tmtt)
REVERT: F  325 LEU cc_start: 0.8630 (mt) cc_final: 0.8410 (mp)
REVERT: F  342 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7580 (pm20)
REVERT: F  375 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7015 (tmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 25
  average time/residue: 0.3875
  time to fit residues: 11.0771
Evaluate side-chains
  27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0370
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    2.8066

-------------------------------------------------------------------------------
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 = 0.4272 r_free = 0.4272 target = 0.122127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.102944 restraints weight = 4636.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.105576 restraints weight = 2208.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.107417 restraints weight = 1448.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3522  Z= 0.243
  Angle     :  0.601   5.177   4710  Z= 0.307
  Chirality :  0.051   0.119    528
  Planarity :  0.003   0.024    600
  Dihedral  :  5.029  14.041    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.33 %
    Favored  : 90.15 %
  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 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 362 
 PHE   0.006   0.001   PHE F 378 
 TYR   0.019   0.005   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
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9137 (mt) cc_final: 0.8778 (mp)
REVERT: D  342 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7381 (pm20)
REVERT: D  375 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7093 (tmtt)
REVERT: F  325 LEU cc_start: 0.8628 (mt) cc_final: 0.8414 (mp)
REVERT: F  342 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7573 (pm20)
REVERT: F  375 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7006 (tmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 26
  average time/residue: 0.3782
  time to fit residues: 11.2681
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  : 0.403 
-------------------------------------------------------------------------------
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 3 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.120125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.101043 restraints weight = 4684.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.103732 restraints weight = 2166.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.105453 restraints weight = 1396.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2467

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= 0.291
  Angle     :  0.632   6.271   4710  Z= 0.326
  Chirality :  0.052   0.120    528
  Planarity :  0.003   0.023    600
  Dihedral  :  5.152  14.329    468
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.33 %
    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: -3.30 (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   0.005   0.001   HIS D 362 
 PHE   0.007   0.002   PHE F 378 
 TYR   0.022   0.005   TYR C 310 
 ARG   0.001   0.000   ARG E 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
  29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9130 (mt) cc_final: 0.8769 (mp)
REVERT: D  342 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7457 (pm20)
REVERT: D  375 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7086 (tmtt)
REVERT: F  325 LEU cc_start: 0.8621 (mt) cc_final: 0.8407 (mp)
REVERT: F  342 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7604 (pm20)
REVERT: F  375 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7013 (tmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 26
  average time/residue: 0.3652
  time to fit residues: 10.8513
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  : 0.386 
-------------------------------------------------------------------------------
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 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 38 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.120953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.101908 restraints weight = 4720.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.104522 restraints weight = 2273.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.106278 restraints weight = 1493.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3522  Z= 0.276
  Angle     :  0.626   6.283   4710  Z= 0.323
  Chirality :  0.052   0.121    528
  Planarity :  0.003   0.031    600
  Dihedral  :  5.154  14.331    468
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.84 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.31 (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   0.005   0.001   HIS D 362 
 PHE   0.007   0.002   PHE F 378 
 TYR   0.023   0.005   TYR C 310 
 ARG   0.001   0.000   ARG F 349 

********************** 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
  28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A  328 ILE cc_start: 0.9137 (mt) cc_final: 0.8777 (mp)
REVERT: D  342 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7443 (pm20)
REVERT: D  375 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7062 (tmtt)
REVERT: F  325 LEU cc_start: 0.8620 (mt) cc_final: 0.8408 (mp)
REVERT: F  342 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7605 (pm20)
REVERT: F  375 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7004 (tmtt)
  outliers start: 6
  outliers final: 6
  residues processed: 25
  average time/residue: 0.3554
  time to fit residues: 10.2327
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  : 0.395 
-------------------------------------------------------------------------------
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 41 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    5.3788

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.117446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.099134 restraints weight = 4934.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.101417 restraints weight = 2519.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.102932 restraints weight = 1699.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   3522  Z= 0.450
  Angle     :  0.732   5.733   4710  Z= 0.386
  Chirality :  0.055   0.129    528
  Planarity :  0.004   0.029    600
  Dihedral  :  5.647  15.173    468
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.71 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.84 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 : -2.70 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   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 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1367.91 seconds
wall clock time: 25 minutes 34.31 seconds (1534.31 seconds total)