Starting phenix.real_space_refine
on Tue Mar  3 12:31:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2026/7p6d_13226.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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      10      5.16       5
     C    2695      2.51       5
     N     810      2.21       5
     O     825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4340
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 868
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.58, per 1000 atoms: 0.13
  Number of scatterers: 4340
  At special positions: 0
  Unit cell: (114.66, 88.92, 43.29, 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      10     16.00
     O     825      8.00
     N     810      7.00
     C    2695      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: 0.36
  Conformation dependent library (CDL) restraints added in 124.8 milliseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 42.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 275 through 283
      removed outlier: 7.070A  pdb=" N   GLN C 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ILE B 277 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ILE C 278 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ASN B 279 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   LYS C 280 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LYS B 281 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   GLN A 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 10.184A  pdb=" N   ASN C 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 9.179A  pdb=" N   ILE A 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 10.431A  pdb=" N   LYS C 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   LYS A 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   ASP C 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLN E 276 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ILE A 277 " --> pdb=" O   GLN E 276 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE E 278 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ASN A 279 " --> pdb=" O   ILE E 278 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LYS E 280 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LYS A 281 " --> pdb=" O   LYS E 280 " (cutoff:3.500A)
      removed outlier: 9.178A  pdb=" N   GLN D 276 " --> pdb=" O   ILE E 277 " (cutoff:3.500A)
      removed outlier: 10.167A  pdb=" N   ASN E 279 " --> pdb=" O   GLN D 276 " (cutoff:3.500A)
      removed outlier: 9.153A  pdb=" N   ILE D 278 " --> pdb=" O   ASN E 279 " (cutoff:3.500A)
      removed outlier: 10.412A  pdb=" N   LYS E 281 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   LYS D 280 " --> pdb=" O   LYS E 281 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   ASP E 283 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU D 282 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 293 through 299
      removed outlier: 6.826A  pdb=" N   SER B 293 " --> pdb=" O   LYS C 294 " (cutoff:3.500A)
      removed outlier: 8.525A  pdb=" N   ASN C 296 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   ASP B 295 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   LYS C 298 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER A 293 " --> pdb=" O   LYS E 294 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   ASN E 296 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ASP A 295 " --> pdb=" O   ASN E 296 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   LYS E 298 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE A 297 " --> pdb=" O   LYS E 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.511A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.934A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 321
      removed outlier: 6.472A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   SER C 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR B 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS A 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   SER E 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR A 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.803A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE D 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 341
      removed outlier: 6.506A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL D 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   LYS E 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL D 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345
      removed outlier: 6.885A  pdb=" N   LEU A 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU D 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 353 through 354
      removed outlier: 6.529A  pdb=" N   LYS B 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS A 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 362
      removed outlier: 6.344A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   THR E 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE D 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 369 through 374
      removed outlier: 6.299A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   HIS C 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LYS A 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   GLU E 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE A 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   HIS E 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   THR A 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 377 through 385
      removed outlier: 6.881A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   GLU C 380 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ARG B 379 " --> pdb=" O   GLU C 380 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   ALA C 382 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASN B 381 " --> pdb=" O   ALA C 382 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   ALA C 384 " --> pdb=" O   ASN B 381 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LYS B 383 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   THR A 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLU E 380 " --> pdb=" O   THR A 377 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ARG A 379 " --> pdb=" O   GLU E 380 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ALA E 382 " --> pdb=" O   ARG A 379 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ASN A 381 " --> pdb=" O   ALA E 382 " (cutoff:3.500A)
      removed outlier: 8.335A  pdb=" N   ALA E 384 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS A 383 " --> pdb=" O   ALA E 384 " (cutoff:3.500A)

    86 hydrogen bonds defined for protein.
    258 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: 0.45

  Time building geometry restraints manager: 0.48 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: 1455
        1.34 -     1.46: 583
        1.46 -     1.57: 2347
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4395
  Sorted by residual:
  bond pdb=" N   VAL D 275 "
       pdb=" CA  VAL D 275 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.035 1.24e-02 6.50e+03 8.16e+00
  bond pdb=" N   VAL A 275 "
       pdb=" CA  VAL A 275 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.24e-02 6.50e+03 7.81e+00
  bond pdb=" N   VAL B 275 "
       pdb=" CA  VAL B 275 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.72e+00
  bond pdb=" N   VAL C 275 "
       pdb=" CA  VAL C 275 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.72e+00
  bond pdb=" N   VAL E 275 "
       pdb=" CA  VAL E 275 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.67e+00
  ... (remaining 4390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 5464
        1.15 -     2.29: 301
        2.29 -     3.44: 90
        3.44 -     4.59: 5
        4.59 -     5.74: 10
  Bond angle restraints: 5870
  Sorted by residual:
  angle pdb=" CA  VAL B 275 "
        pdb=" C   VAL B 275 "
        pdb=" O   VAL B 275 "
      ideal   model   delta    sigma   weight residual
     120.53  117.28    3.25 1.07e+00 8.73e-01 9.24e+00
  angle pdb=" CA  VAL E 275 "
        pdb=" C   VAL E 275 "
        pdb=" O   VAL E 275 "
      ideal   model   delta    sigma   weight residual
     120.53  117.29    3.24 1.07e+00 8.73e-01 9.18e+00
  angle pdb=" CA  VAL C 275 "
        pdb=" C   VAL C 275 "
        pdb=" O   VAL C 275 "
      ideal   model   delta    sigma   weight residual
     120.53  117.31    3.22 1.07e+00 8.73e-01 9.07e+00
  angle pdb=" CA  VAL A 275 "
        pdb=" C   VAL A 275 "
        pdb=" O   VAL A 275 "
      ideal   model   delta    sigma   weight residual
     120.53  117.32    3.21 1.07e+00 8.73e-01 9.00e+00
  angle pdb=" CA  VAL D 275 "
        pdb=" C   VAL D 275 "
        pdb=" O   VAL D 275 "
      ideal   model   delta    sigma   weight residual
     120.53  117.34    3.19 1.07e+00 8.73e-01 8.90e+00
  ... (remaining 5865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 2530
       16.00 -    32.00: 150
       32.00 -    47.99: 35
       47.99 -    63.99: 0
       63.99 -    79.99: 5
  Dihedral angle restraints: 2720
    sinusoidal: 1135
      harmonic: 1585
  Sorted by residual:
  dihedral pdb=" CB  GLU A 342 "
           pdb=" CG  GLU A 342 "
           pdb=" CD  GLU A 342 "
           pdb=" OE1 GLU A 342 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.99   79.99     1      3.00e+01 1.11e-03 8.81e+00
  dihedral pdb=" CB  GLU E 342 "
           pdb=" CG  GLU E 342 "
           pdb=" CD  GLU E 342 "
           pdb=" OE1 GLU E 342 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.98   79.98     1      3.00e+01 1.11e-03 8.81e+00
  dihedral pdb=" CB  GLU D 342 "
           pdb=" CG  GLU D 342 "
           pdb=" CD  GLU D 342 "
           pdb=" OE1 GLU D 342 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.98   79.98     1      3.00e+01 1.11e-03 8.81e+00
  ... (remaining 2717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 410
       0.037 -    0.074: 130
       0.074 -    0.112: 83
       0.112 -    0.149: 32
       0.149 -    0.186: 5
  Chirality restraints: 660
  Sorted by residual:
  chirality pdb=" CA  VAL E 275 "
            pdb=" N   VAL E 275 "
            pdb=" C   VAL E 275 "
            pdb=" CB  VAL E 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.64e-01
  chirality pdb=" CA  VAL C 275 "
            pdb=" N   VAL C 275 "
            pdb=" C   VAL C 275 "
            pdb=" CB  VAL C 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CA  VAL D 275 "
            pdb=" N   VAL D 275 "
            pdb=" C   VAL D 275 "
            pdb=" CB  VAL D 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 657 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 361 "    0.003 2.00e-02 2.50e+03   6.27e-03 3.93e-01
        pdb=" C   THR A 361 "   -0.011 2.00e-02 2.50e+03
        pdb=" O   THR A 361 "    0.004 2.00e-02 2.50e+03
        pdb=" N   HIS A 362 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 300 "   -0.010 5.00e-02 4.00e+02   1.56e-02 3.89e-01
        pdb=" N   PRO E 301 "    0.027 5.00e-02 4.00e+02
        pdb=" CA  PRO E 301 "   -0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO E 301 "   -0.009 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 361 "    0.003 2.00e-02 2.50e+03   6.21e-03 3.85e-01
        pdb=" C   THR D 361 "   -0.011 2.00e-02 2.50e+03
        pdb=" O   THR D 361 "    0.004 2.00e-02 2.50e+03
        pdb=" N   HIS D 362 "    0.004 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.04: 2321
        3.04 -     3.51: 3873
        3.51 -     3.97: 6583
        3.97 -     4.44: 6965
        4.44 -     4.90: 12089
  Nonbonded interactions: 31831
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 305 "
            pdb=" O   GLY C 303 "
     model   vdw
     2.575 3.040
  nonbonded pdb=" O   GLY B 303 "
            pdb=" OG  SER C 305 "
     model   vdw
     2.579 3.040
  nonbonded pdb=" O   GLY A 303 "
            pdb=" OG  SER E 305 "
     model   vdw
     2.584 3.040
  nonbonded pdb=" OG1 THR A 386 "
            pdb=" N   ASP A 387 "
     model   vdw
     2.587 3.120
  nonbonded pdb=" OG1 THR E 386 "
            pdb=" N   ASP E 387 "
     model   vdw
     2.588 3.120
  ... (remaining 31826 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.170
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.003   0.035   4395  Z= 0.204
  Angle     :  0.655   5.737   5870  Z= 0.382
  Chirality :  0.054   0.186    660
  Planarity :  0.002   0.016    755
  Dihedral  : 11.405  79.990   1710
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.003   0.001   TYR D 310 
 PHE   0.006   0.001   PHE B 378 
 HIS   0.002   0.000   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4395)
  covalent geometry    : angle       0.65519 ( 5870)
  hydrogen bonds       : bond        0.22191 (   86)
  hydrogen bonds       : angle       7.67187 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.179 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0609
  time to fit residues: 5.1584
Evaluate side-chains
  43 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    1.5992

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

Flipped N/Q/H residues before XYZ refinement:
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 299 HIS
D 362 HIS
E 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.103551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.086552 restraints weight = 6612.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.95
r_work: 0.3432 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4395  Z= 0.104
  Angle     :  0.501   5.102   5870  Z= 0.263
  Chirality :  0.051   0.119    660
  Planarity :  0.002   0.026    755
  Dihedral  :  4.127  13.842    585
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.04 %
    Favored  : 95.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.32), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.010   0.002   TYR D 310 
 PHE   0.012   0.002   PHE D 346 
 HIS   0.011   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4395)
  covalent geometry    : angle       0.50107 ( 5870)
  hydrogen bonds       : bond        0.01913 (   86)
  hydrogen bonds       : angle       4.85657 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.6820 (mtt-85)
REVERT: C  281 LYS cc_start: 0.8207 (mttt) cc_final: 0.7929 (mttp)
REVERT: C  338 GLU cc_start: 0.7810 (tt0) cc_final: 0.6918 (mt-10)
REVERT: E  276 GLN cc_start: 0.7808 (mt0) cc_final: 0.7551 (mt0)
REVERT: E  349 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7161 (mtt90)
  outliers start: 1
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0543
  time to fit residues: 3.1456
Evaluate side-chains
  35 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0170
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    2.4026

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.099797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.083179 restraints weight = 6749.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.87
r_work: 0.3385 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4395  Z= 0.129
  Angle     :  0.495   4.069   5870  Z= 0.263
  Chirality :  0.051   0.121    660
  Planarity :  0.002   0.017    755
  Dihedral  :  4.321  12.947    585
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.67 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.32), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.008   0.002   TYR E 310 
 PHE   0.011   0.002   PHE A 346 
 HIS   0.008   0.002   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4395)
  covalent geometry    : angle       0.49496 ( 5870)
  hydrogen bonds       : bond        0.01870 (   86)
  hydrogen bonds       : angle       4.42775 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.193 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.6843 (mtt-85)
REVERT: C  338 GLU cc_start: 0.8359 (tt0) cc_final: 0.7566 (mt-10)
REVERT: D  349 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7577 (mtm180)
REVERT: D  362 HIS cc_start: 0.8580 (t-90) cc_final: 0.8310 (t-90)
REVERT: E  276 GLN cc_start: 0.7855 (mt0) cc_final: 0.7634 (mt0)
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.0735
  time to fit residues: 4.4785
Evaluate side-chains
  42 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
C 351 GLN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.097458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.080640 restraints weight = 6668.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.85
r_work: 0.3335 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   4395  Z= 0.199
  Angle     :  0.550   5.858   5870  Z= 0.294
  Chirality :  0.052   0.128    660
  Planarity :  0.002   0.019    755
  Dihedral  :  4.758  14.859    585
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 349 
 TYR   0.010   0.002   TYR A 310 
 PHE   0.013   0.003   PHE B 378 
 HIS   0.007   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 4395)
  covalent geometry    : angle       0.54985 ( 5870)
  hydrogen bonds       : bond        0.02145 (   86)
  hydrogen bonds       : angle       4.41881 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  385 LYS cc_start: 0.7229 (tttt) cc_final: 0.6836 (tptp)
REVERT: B  349 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.6763 (mtt-85)
REVERT: B  371 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7386 (mt)
REVERT: B  385 LYS cc_start: 0.7203 (tttt) cc_final: 0.6844 (tptp)
REVERT: C  338 GLU cc_start: 0.8255 (tt0) cc_final: 0.7474 (mt-10)
REVERT: C  349 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7716 (mtp85)
REVERT: D  349 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7711 (mtm180)
REVERT: E  276 GLN cc_start: 0.7862 (mt0) cc_final: 0.7620 (mt0)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 0.0859
  time to fit residues: 5.3243
Evaluate side-chains
  46 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  377 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 374 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.098354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.081789 restraints weight = 6761.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.89
r_work: 0.3370 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4395  Z= 0.126
  Angle     :  0.495   6.544   5870  Z= 0.259
  Chirality :  0.051   0.126    660
  Planarity :  0.002   0.014    755
  Dihedral  :  4.443  12.870    585
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.29 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.011   0.002   TYR A 310 
 PHE   0.009   0.002   PHE E 378 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4395)
  covalent geometry    : angle       0.49475 ( 5870)
  hydrogen bonds       : bond        0.01601 (   86)
  hydrogen bonds       : angle       4.17676 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.174 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.6715 (mtt-85)
REVERT: C  338 GLU cc_start: 0.8365 (tt0) cc_final: 0.7576 (mt-10)
REVERT: C  349 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7638 (mtp85)
REVERT: D  349 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7740 (mtm180)
REVERT: D  371 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7795 (mp)
REVERT: E  276 GLN cc_start: 0.7865 (mt0) cc_final: 0.7646 (mt0)
  outliers start: 7
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0730
  time to fit residues: 4.1194
Evaluate side-chains
  43 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.094493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.077528 restraints weight = 7020.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.84
r_work: 0.3281 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.040   4395  Z= 0.328
  Angle     :  0.654   7.320   5870  Z= 0.353
  Chirality :  0.055   0.165    660
  Planarity :  0.003   0.018    755
  Dihedral  :  5.255  16.482    585
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.20 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 10.10 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 349 
 TYR   0.012   0.002   TYR A 310 
 PHE   0.019   0.004   PHE B 378 
 HIS   0.010   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 ( 4395)
  covalent geometry    : angle       0.65447 ( 5870)
  hydrogen bonds       : bond        0.02913 (   86)
  hydrogen bonds       : angle       4.51311 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7757 (mtp85)
REVERT: A  385 LYS cc_start: 0.7275 (tttt) cc_final: 0.6849 (tptp)
REVERT: B  349 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7066 (mtt-85)
REVERT: C  338 GLU cc_start: 0.8360 (tt0) cc_final: 0.7646 (mt-10)
REVERT: C  349 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7825 (mtp85)
REVERT: D  349 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7862 (mtm180)
REVERT: E  276 GLN cc_start: 0.7987 (mt0) cc_final: 0.7757 (mt0)
REVERT: E  344 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8204 (tp)
REVERT: E  349 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7904 (mtt90)
  outliers start: 15
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0811
  time to fit residues: 4.9060
Evaluate side-chains
  47 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  344 LEU
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  377 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 31 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.095156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.078149 restraints weight = 6958.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.84
r_work: 0.3319 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   4395  Z= 0.269
  Angle     :  0.617   6.576   5870  Z= 0.331
  Chirality :  0.053   0.132    660
  Planarity :  0.003   0.022    755
  Dihedral  :  5.081  15.193    585
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.91 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.014   0.003   TYR E 310 
 PHE   0.015   0.004   PHE B 378 
 HIS   0.008   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 4395)
  covalent geometry    : angle       0.61686 ( 5870)
  hydrogen bonds       : bond        0.02564 (   86)
  hydrogen bonds       : angle       4.52592 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7813 (mtp85)
REVERT: B  349 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7130 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7377 (tttt) cc_final: 0.6946 (tptp)
REVERT: C  338 GLU cc_start: 0.8289 (tt0) cc_final: 0.7651 (mt-10)
REVERT: C  349 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7914 (mtp85)
REVERT: D  349 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7961 (mtm180)
REVERT: E  276 GLN cc_start: 0.8043 (mt0) cc_final: 0.7813 (mt0)
REVERT: E  349 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7996 (mtt90)
REVERT: E  360 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7751 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0844
  time to fit residues: 5.1444
Evaluate side-chains
  48 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  377 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.096381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079294 restraints weight = 6889.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.88
r_work: 0.3327 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4395  Z= 0.185
  Angle     :  0.552   7.042   5870  Z= 0.291
  Chirality :  0.052   0.130    660
  Planarity :  0.002   0.020    755
  Dihedral  :  4.836  14.702    585
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.91 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.011   0.003   PHE E 378 
 HIS   0.006   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 4395)
  covalent geometry    : angle       0.55245 ( 5870)
  hydrogen bonds       : bond        0.02070 (   86)
  hydrogen bonds       : angle       4.32352 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7798 (mtp85)
REVERT: B  349 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7048 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7297 (tttt) cc_final: 0.6869 (tptp)
REVERT: C  338 GLU cc_start: 0.8328 (tt0) cc_final: 0.7601 (mt-10)
REVERT: C  349 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7841 (mtp85)
REVERT: D  349 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.7929 (mtm180)
REVERT: D  371 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7630 (mp)
REVERT: E  276 GLN cc_start: 0.7968 (mt0) cc_final: 0.7748 (mt0)
REVERT: E  349 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7848 (mtt90)
REVERT: E  360 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7456 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 48
  average time/residue: 0.0876
  time to fit residues: 5.3155
Evaluate side-chains
  48 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  377 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.097689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.080613 restraints weight = 6863.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.91
r_work: 0.3351 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4395  Z= 0.132
  Angle     :  0.514   7.238   5870  Z= 0.268
  Chirality :  0.051   0.132    660
  Planarity :  0.002   0.019    755
  Dihedral  :  4.571  13.230    585
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.52 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.009   0.002   PHE E 378 
 HIS   0.005   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4395)
  covalent geometry    : angle       0.51421 ( 5870)
  hydrogen bonds       : bond        0.01668 (   86)
  hydrogen bonds       : angle       4.10953 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7813 (mtp85)
REVERT: B  349 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7100 (mtt-85)
REVERT: B  371 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7506 (mt)
REVERT: C  338 GLU cc_start: 0.8300 (tt0) cc_final: 0.7592 (mt-10)
REVERT: C  349 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7749 (mtp85)
REVERT: D  349 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7841 (mtm180)
REVERT: D  371 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7665 (mp)
REVERT: E  276 GLN cc_start: 0.7940 (mt0) cc_final: 0.7733 (mt0)
REVERT: E  349 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7852 (mtt90)
  outliers start: 9
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0780
  time to fit residues: 4.7073
Evaluate side-chains
  47 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.095619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078412 restraints weight = 6938.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.89
r_work: 0.3290 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   4395  Z= 0.308
  Angle     :  0.642   7.306   5870  Z= 0.345
  Chirality :  0.054   0.134    660
  Planarity :  0.003   0.022    755
  Dihedral  :  5.192  15.975    585
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.80 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.12 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.018   0.004   PHE B 378 
 HIS   0.009   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00704 ( 4395)
  covalent geometry    : angle       0.64173 ( 5870)
  hydrogen bonds       : bond        0.02843 (   86)
  hydrogen bonds       : angle       4.34491 (  258)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7836 (mtp85)
REVERT: B  349 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7127 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7339 (tttt) cc_final: 0.6889 (tptp)
REVERT: C  338 GLU cc_start: 0.8295 (tt0) cc_final: 0.7624 (mt-10)
REVERT: C  349 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7875 (mtp85)
REVERT: D  274 LYS cc_start: 0.8477 (mptt) cc_final: 0.7836 (mmtm)
REVERT: D  349 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8023 (mtm180)
REVERT: E  276 GLN cc_start: 0.7966 (mt0) cc_final: 0.7731 (mt0)
  outliers start: 9
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0773
  time to fit residues: 4.6590
Evaluate side-chains
  49 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  371 ILE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.095318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.078205 restraints weight = 7007.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.84
r_work: 0.3295 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   4395  Z= 0.290
  Angle     :  0.633   7.385   5870  Z= 0.340
  Chirality :  0.054   0.133    660
  Planarity :  0.003   0.026    755
  Dihedral  :  5.144  15.353    585
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.92 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.017   0.004   PHE D 378 
 HIS   0.008   0.002   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 4395)
  covalent geometry    : angle       0.63285 ( 5870)
  hydrogen bonds       : bond        0.02758 (   86)
  hydrogen bonds       : angle       4.39837 (  258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1285.91 seconds
wall clock time: 22 minutes 44.16 seconds (1364.16 seconds total)