Starting phenix.real_space_refine
on Tue Feb 11 05:43:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p6d_13226/02_2025/7p6d_13226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p6d_13226/02_2025/7p6d_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_13226/02_2025/7p6d_13226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p6d_13226/02_2025/7p6d_13226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p6d_13226/02_2025/7p6d_13226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p6d_13226/02_2025/7p6d_13226.cif"
  }
  resolution = 3.3
  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=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, D
  Time building chain proxies: 2.21, per 1000 atoms: 0.51
  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: 0.88
  Conformation dependent library (CDL) restraints added in 512.6 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: 0.62
  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: 1.09

  Time building geometry restraints manager: 1.06 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             0.470
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.220
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.810
-------------------------------------------------------------------------------
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= 0.209
  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 (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: -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
 HIS   0.002   0.000   HIS D 299 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.001   0.000   ARG B 349 

*********************** 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  : 0.541 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1452
  time to fit residues: 12.1898
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  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0000
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   overall best weight:    5.1992

-------------------------------------------------------------------------------
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**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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 = 0.097304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.080354 restraints weight = 6749.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.88
r_work: 0.3347 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4395  Z= 0.416
  Angle     :  0.634   4.891   5870  Z= 0.342
  Chirality :  0.054   0.141    660
  Planarity :  0.003   0.028    755
  Dihedral  :  5.099  16.178    585
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  7.26 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.66 %
    Favored  : 93.74 %
  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: -2.65 (0.32), 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
 HIS   0.011   0.003   HIS C 299 
 PHE   0.017   0.004   PHE B 346 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.002   0.000   ARG E 349 

*********************** 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
  54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  385 LYS cc_start: 0.7277 (tttt) cc_final: 0.6877 (tptp)
REVERT: B  349 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7082 (mtt-85)
REVERT: B  362 HIS cc_start: 0.9013 (t70) cc_final: 0.8737 (t-170)
REVERT: C  338 GLU cc_start: 0.8324 (tt0) cc_final: 0.7570 (mt-10)
REVERT: C  349 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7832 (mtp85)
REVERT: D  349 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7622 (mtm180)
REVERT: E  276 GLN cc_start: 0.7903 (mt0) cc_final: 0.6964 (mp10)
  outliers start: 3
  outliers final: 2
  residues processed: 54
  average time/residue: 0.1815
  time to fit residues: 12.5334
Evaluate side-chains
  45 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain E residue  377 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 374 HIS
D 362 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.097978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.081222 restraints weight = 6723.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.87
r_work: 0.3342 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4395  Z= 0.260
  Angle     :  0.538   5.753   5870  Z= 0.286
  Chirality :  0.051   0.124    660
  Planarity :  0.002   0.017    755
  Dihedral  :  4.669  14.249    585
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  9.49 %
    Favored  : 89.49 %
  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: -2.69 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 299 
 PHE   0.012   0.003   PHE E 378 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.001   0.000   ARG E 349 

*********************** 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
  46 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.493 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.6839 (mtt-85)
REVERT: B  371 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7365 (mt)
REVERT: C  338 GLU cc_start: 0.8317 (tt0) cc_final: 0.7558 (mt-10)
REVERT: C  349 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7731 (mtp85)
REVERT: D  349 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7721 (mtm180)
REVERT: D  371 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: E  276 GLN cc_start: 0.7873 (mt0) cc_final: 0.7613 (mt0)
REVERT: E  349 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7648 (mtp85)
  outliers start: 5
  outliers final: 2
  residues processed: 46
  average time/residue: 0.1606
  time to fit residues: 9.8321
Evaluate side-chains
  43 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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  371 ILE
Chi-restraints excluded: chain D residue  371 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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**
** 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 = 0.3639 r_free = 0.3639 target = 0.094288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.077361 restraints weight = 6965.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.81
r_work: 0.3279 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.044   4395  Z= 0.556
  Angle     :  0.687   5.990   5870  Z= 0.372
  Chirality :  0.056   0.169    660
  Planarity :  0.003   0.020    755
  Dihedral  :  5.461  16.000    585
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.93 %
    Favored  : 84.44 %
  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: -3.01 (0.31), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS C 330 
 PHE   0.020   0.004   PHE B 378 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

*********************** 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
  51 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7942 (mtp85)
REVERT: B  349 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7161 (mtt-85)
REVERT: C  338 GLU cc_start: 0.8277 (tt0) cc_final: 0.7580 (mt-10)
REVERT: C  349 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7982 (mtp85)
REVERT: D  349 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7816 (mtm180)
REVERT: E  276 GLN cc_start: 0.8066 (mt0) cc_final: 0.7799 (mt0)
REVERT: E  349 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7827 (mtt90)
REVERT: E  360 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7822 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 51
  average time/residue: 0.1746
  time to fit residues: 11.6057
Evaluate side-chains
  47 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
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  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  371 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 40 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3719 r_free = 0.3719 target = 0.098139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.081185 restraints weight = 6894.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.91
r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2639

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= 0.207
  Angle     :  0.517   5.876   5870  Z= 0.271
  Chirality :  0.051   0.133    660
  Planarity :  0.002   0.017    755
  Dihedral  :  4.631  13.472    585
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.53 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 299 
 PHE   0.009   0.002   PHE E 378 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  51 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7811 (mtp85)
REVERT: B  349 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7024 (mtt-85)
REVERT: B  371 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: C  349 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7732 (mtp85)
REVERT: D  349 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7743 (mtm180)
REVERT: D  360 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8071 (mt)
REVERT: E  276 GLN cc_start: 0.7948 (mt0) cc_final: 0.7732 (mt0)
REVERT: E  349 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7522 (mtt90)
  outliers start: 9
  outliers final: 6
  residues processed: 50
  average time/residue: 0.1885
  time to fit residues: 12.1907
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  : 0.551 
-------------------------------------------------------------------------------
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 E residue  377 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 7 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0020
   chunk 22 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 362 HIS
C 362 HIS
E 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.096668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.079668 restraints weight = 6786.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.88
r_work: 0.3332 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2789

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= 0.289
  Angle     :  0.547   5.740   5870  Z= 0.288
  Chirality :  0.051   0.132    660
  Planarity :  0.002   0.016    755
  Dihedral  :  4.777  14.489    585
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 11.52 %
    Favored  : 85.25 %
  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: -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
 HIS   0.006   0.001   HIS B 330 
 PHE   0.012   0.003   PHE B 378 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

*********************** 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
  55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7820 (mtp85)
REVERT: B  349 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7039 (mtt-85)
REVERT: C  349 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7797 (mtp85)
REVERT: D  342 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7743 (tm-30)
REVERT: D  349 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7780 (mtm180)
REVERT: D  360 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7933 (mt)
REVERT: D  371 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: E  276 GLN cc_start: 0.7969 (mt0) cc_final: 0.7745 (mt0)
REVERT: E  349 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7520 (mtt90)
REVERT: E  360 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7402 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1804
  time to fit residues: 12.1540
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  : 0.539 
-------------------------------------------------------------------------------
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  314 ASP
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  342 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.096483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.079386 restraints weight = 6822.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.87
r_work: 0.3321 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4395  Z= 0.317
  Angle     :  0.564   5.906   5870  Z= 0.297
  Chirality :  0.052   0.132    660
  Planarity :  0.002   0.016    755
  Dihedral  :  4.808  14.400    585
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.92 %
    Favored  : 85.05 %
  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: -2.98 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B 330 
 PHE   0.012   0.003   PHE B 378 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7871 (mtp85)
REVERT: B  349 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7083 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7324 (tttt) cc_final: 0.6893 (tptp)
REVERT: C  325 LEU cc_start: 0.7774 (mp) cc_final: 0.7364 (tt)
REVERT: C  349 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7853 (mtp85)
REVERT: D  342 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7678 (tm-30)
REVERT: D  349 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.7876 (mtm180)
REVERT: D  371 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7619 (mp)
REVERT: E  276 GLN cc_start: 0.8005 (mt0) cc_final: 0.7784 (mt0)
REVERT: E  349 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7678 (mtt90)
REVERT: E  360 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7360 (mt)
  outliers start: 15
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1767
  time to fit residues: 11.5131
Evaluate side-chains
  52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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  314 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  342 GLU
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 45 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.094863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.077796 restraints weight = 6903.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.86
r_work: 0.3297 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   4395  Z= 0.481
  Angle     :  0.648   5.881   5870  Z= 0.347
  Chirality :  0.054   0.134    660
  Planarity :  0.003   0.019    755
  Dihedral  :  5.270  16.271    585
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.13 %
    Favored  : 84.24 %
  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: -3.17 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS C 330 
 PHE   0.018   0.004   PHE D 378 
 TYR   0.014   0.003   TYR A 310 
 ARG   0.002   0.001   ARG A 379 

*********************** 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
  56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.486 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7162 (mtt-85)
REVERT: C  325 LEU cc_start: 0.7907 (mp) cc_final: 0.7391 (tt)
REVERT: C  349 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7863 (mtp85)
REVERT: D  274 LYS cc_start: 0.8479 (mptt) cc_final: 0.7819 (mmtm)
REVERT: D  342 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7700 (tm-30)
REVERT: D  349 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.7957 (mtm180)
REVERT: D  371 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: E  276 GLN cc_start: 0.7965 (mt0) cc_final: 0.7717 (mt0)
REVERT: E  349 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7993 (mtt90)
  outliers start: 13
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1781
  time to fit residues: 12.3394
Evaluate side-chains
  53 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
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  360 ILE
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  342 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.095560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.078404 restraints weight = 6932.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.87
r_work: 0.3300 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4395  Z= 0.406
  Angle     :  0.611   6.016   5870  Z= 0.326
  Chirality :  0.053   0.134    660
  Planarity :  0.003   0.028    755
  Dihedral  :  5.093  15.231    585
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.32 %
    Favored  : 84.65 %
  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: -3.19 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 330 
 PHE   0.015   0.003   PHE B 378 
 TYR   0.014   0.003   TYR A 310 
 ARG   0.003   0.001   ARG A 349 

*********************** 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
  57 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.512 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7114 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7269 (tttt) cc_final: 0.6803 (tptp)
REVERT: C  325 LEU cc_start: 0.7940 (mp) cc_final: 0.7453 (tt)
REVERT: C  349 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7959 (mtp85)
REVERT: D  274 LYS cc_start: 0.8485 (mptt) cc_final: 0.7852 (mmtm)
REVERT: D  342 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7682 (tm-30)
REVERT: D  349 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.7912 (mtm180)
REVERT: D  371 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7637 (mp)
REVERT: E  276 GLN cc_start: 0.8107 (mt0) cc_final: 0.7875 (mt0)
REVERT: E  349 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8131 (mtt90)
REVERT: E  360 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7392 (mt)
  outliers start: 15
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1939
  time to fit residues: 13.4730
Evaluate side-chains
  56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
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  314 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  276 GLN
Chi-restraints excluded: chain D residue  342 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.097007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.079902 restraints weight = 6714.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.84
r_work: 0.3348 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4395  Z= 0.242
  Angle     :  0.543   6.285   5870  Z= 0.282
  Chirality :  0.052   0.134    660
  Planarity :  0.003   0.034    755
  Dihedral  :  4.740  14.120    585
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.93 %
    Favored  : 84.65 %
  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: -3.10 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 299 
 PHE   0.010   0.002   PHE E 378 
 TYR   0.014   0.003   TYR A 310 
 ARG   0.004   0.001   ARG A 349 

********************** 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
  56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.494 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7123 (mtt-85)
REVERT: B  385 LYS cc_start: 0.7304 (tttt) cc_final: 0.6889 (tptp)
REVERT: C  325 LEU cc_start: 0.7952 (mp) cc_final: 0.7460 (tt)
REVERT: D  342 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7680 (tm-30)
REVERT: D  349 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7831 (mtm180)
REVERT: D  360 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7995 (mt)
REVERT: D  371 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7698 (mp)
REVERT: E  276 GLN cc_start: 0.7998 (mt0) cc_final: 0.7777 (mt0)
REVERT: E  349 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7961 (mtt90)
REVERT: E  360 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7365 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 55
  average time/residue: 0.1806
  time to fit residues: 12.7169
Evaluate side-chains
  52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  342 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.095294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.078344 restraints weight = 6876.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.80
r_work: 0.3311 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4395  Z= 0.405
  Angle     :  0.611   6.053   5870  Z= 0.325
  Chirality :  0.053   0.135    660
  Planarity :  0.003   0.033    755
  Dihedral  :  5.044  15.344    585
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.15 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.73 %
    Favored  : 84.44 %
  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: -3.19 (0.30), residues: 565
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.42 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 330 
 PHE   0.015   0.003   PHE D 378 
 TYR   0.014   0.003   TYR A 310 
 ARG   0.007   0.001   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2585.97 seconds
wall clock time: 46 minutes 40.86 seconds (2800.86 seconds total)