Starting phenix.real_space_refine
on Tue Feb 11 04:47:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8otj_17181/02_2025/8otj_17181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8otj_17181/02_2025/8otj_17181.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/8otj_17181/02_2025/8otj_17181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8otj_17181/02_2025/8otj_17181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8otj_17181/02_2025/8otj_17181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8otj_17181/02_2025/8otj_17181.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=   0.000 sd=   0.003
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       7      5.16       5
     C    2569      2.51       5
     N     756      2.21       5
     O     777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 4109
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 2.97, per 1000 atoms: 0.72
  Number of scatterers: 4109
  At special positions: 0
  Unit cell: (132.986, 108.206, 40.474, 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       7     16.00
     O     777      8.00
     N     756      7.00
     C    2569      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: 0.84
  Conformation dependent library (CDL) restraints added in 496.1 milliseconds
  

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 48.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.251A  pdb=" N   VAL A 306 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   VAL B 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE A 308 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 7.043A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324
      removed outlier: 6.303A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   LYS B 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER A 320 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY B 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   CYS A 322 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER E 324 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER F 324 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.072A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.432A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 346
      removed outlier: 6.557A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 359
      removed outlier: 6.342A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS B 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER A 352 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLY B 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 10.592A  pdb=" N   ASN B 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   ASP A 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER E 356 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU A 357 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP E 358 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN A 359 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER F 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU E 357 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP F 358 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN E 359 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 373
      removed outlier: 6.366A  pdb=" N   ASN A 368 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE B 371 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS A 370 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   THR B 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU A 372 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 378 through 379
      removed outlier: 6.560A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.251A  pdb=" N   VAL C 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL G 309 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE C 308 " --> pdb=" O   VAL G 309 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 7.044A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 324
      removed outlier: 6.802A  pdb=" N   SER D 324 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL C 318 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   LYS G 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER C 320 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY G 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   CYS C 322 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.073A  pdb=" N   ILE C 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 340
      removed outlier: 6.431A  pdb=" N   VAL C 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   LYS G 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL C 339 " --> pdb=" O   LYS G 340 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 343 through 346
      removed outlier: 6.558A  pdb=" N   LEU C 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 349 through 359
      removed outlier: 6.783A  pdb=" N   SER D 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU C 357 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP D 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN C 359 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL C 350 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS G 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER C 352 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLY G 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE C 354 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LEU G 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   SER C 356 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 10.593A  pdb=" N   ASN G 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 9.431A  pdb=" N   ASP C 358 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 368 through 373
      removed outlier: 6.365A  pdb=" N   ASN C 368 " --> pdb=" O   LYS G 369 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE G 371 " --> pdb=" O   ASN C 368 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS C 370 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   THR G 373 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   GLU C 372 " --> pdb=" O   THR G 373 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 378 through 379
      removed outlier: 6.560A  pdb=" N   PHE C 378 " --> pdb=" O   ARG G 379 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    285 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: 0.99

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1175
        1.34 -     1.46: 973
        1.46 -     1.58: 2017
        1.58 -     1.70: 0
        1.70 -     1.82: 7
  Bond restraints: 4172
  Sorted by residual:
  bond pdb=" C   LYS D 331 "
       pdb=" N   PRO D 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.364 -0.032 1.28e-02 6.10e+03 6.39e+00
  bond pdb=" C   LYS B 331 "
       pdb=" N   PRO B 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.364 -0.032 1.28e-02 6.10e+03 6.32e+00
  bond pdb=" C   LYS E 331 "
       pdb=" N   PRO E 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.24e+00
  bond pdb=" C   LYS G 331 "
       pdb=" N   PRO G 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.23e+00
  bond pdb=" C   LYS A 331 "
       pdb=" N   PRO A 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.21e+00
  ... (remaining 4167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 4244
        1.87 -     3.73: 1006
        3.73 -     5.60: 287
        5.60 -     7.47: 21
        7.47 -     9.34: 21
  Bond angle restraints: 5579
  Sorted by residual:
  angle pdb=" C   LYS E 321 "
        pdb=" CA  LYS E 321 "
        pdb=" CB  LYS E 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.87   -9.34 1.65e+00 3.67e-01 3.20e+01
  angle pdb=" C   LYS B 321 "
        pdb=" CA  LYS B 321 "
        pdb=" CB  LYS B 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS F 321 "
        pdb=" CA  LYS F 321 "
        pdb=" CB  LYS F 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS D 321 "
        pdb=" CA  LYS D 321 "
        pdb=" CB  LYS D 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" CB  LYS A 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.84   -9.31 1.65e+00 3.67e-01 3.19e+01
  ... (remaining 5574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    12.37: 2058
       12.37 -    24.74: 301
       24.74 -    37.10: 98
       37.10 -    49.47: 49
       49.47 -    61.84: 35
  Dihedral angle restraints: 2541
    sinusoidal: 1064
      harmonic: 1477
  Sorted by residual:
  dihedral pdb=" CA  VAL E 318 "
           pdb=" C   VAL E 318 "
           pdb=" N   THR E 319 "
           pdb=" CA  THR E 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.72  -35.28     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  VAL G 318 "
           pdb=" C   VAL G 318 "
           pdb=" N   THR G 319 "
           pdb=" CA  THR G 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.73  -35.27     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  VAL A 318 "
           pdb=" C   VAL A 318 "
           pdb=" N   THR A 319 "
           pdb=" CA  THR A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.76  -35.24     0      5.00e+00 4.00e-02 4.97e+01
  ... (remaining 2538 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 282
       0.066 -    0.133: 229
       0.133 -    0.199: 63
       0.199 -    0.265: 35
       0.265 -    0.331: 14
  Chirality restraints: 623
  Sorted by residual:
  chirality pdb=" CA  ASP F 348 "
            pdb=" N   ASP F 348 "
            pdb=" C   ASP F 348 "
            pdb=" CB  ASP F 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  ASP E 348 "
            pdb=" N   ASP E 348 "
            pdb=" C   ASP E 348 "
            pdb=" CB  ASP E 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CA  ASP G 348 "
            pdb=" N   ASP G 348 "
            pdb=" C   ASP G 348 "
            pdb=" CB  ASP G 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 620 not shown)

  Planarity restraints: 714
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 331 "   -0.016 2.00e-02 2.50e+03   3.07e-02 9.40e+00
        pdb=" C   LYS E 331 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LYS E 331 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PRO E 332 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS G 331 "    0.016 2.00e-02 2.50e+03   3.06e-02 9.39e+00
        pdb=" C   LYS G 331 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LYS G 331 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO G 332 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 331 "    0.016 2.00e-02 2.50e+03   3.06e-02 9.34e+00
        pdb=" C   LYS D 331 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LYS D 331 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO D 332 "    0.018 2.00e-02 2.50e+03
  ... (remaining 711 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1330
        2.90 -     3.40: 3897
        3.40 -     3.90: 6454
        3.90 -     4.40: 6775
        4.40 -     4.90: 14122
  Nonbonded interactions: 32578
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 353 "
            pdb=" OD2 ASP B 358 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" NZ  LYS C 353 "
            pdb=" OD2 ASP C 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS E 353 "
            pdb=" OD2 ASP E 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS G 353 "
            pdb=" OD2 ASP G 358 "
     model   vdw
     2.401 3.120
  ... (remaining 32573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.130
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.810
  Find NCS groups from input model:        0.090
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
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      :  0.008   0.034   4172  Z= 0.547
  Angle     :  1.799   9.336   5579  Z= 1.104
  Chirality :  0.107   0.331    623
  Planarity :  0.012   0.081    714
  Dihedral  : 16.482  61.835   1603
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  :  8.96 %
    Favored  : 86.57 %
  Cbeta Deviations :  1.49 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.37 %

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: -5.06 (0.19), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.14), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D 330 
 PHE   0.024   0.008   PHE G 346 
 TYR   0.014   0.006   TYR C 310 
 ARG   0.012   0.003   ARG C 349 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  305 SER cc_start: 0.8851 (p) cc_final: 0.8301 (p)
REVERT: A  307 GLN cc_start: 0.8799 (mt0) cc_final: 0.8352 (mp10)
REVERT: A  317 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7347 (ptpp)
REVERT: A  321 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8077 (mttp)
REVERT: A  342 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8266 (mm-30)
REVERT: A  347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8382 (mtpt)
REVERT: B  307 GLN cc_start: 0.8680 (mt0) cc_final: 0.8462 (mp10)
REVERT: B  317 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7589 (ptpp)
REVERT: B  321 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8142 (mttm)
REVERT: B  347 LYS cc_start: 0.8481 (tttt) cc_final: 0.8160 (mtpt)
REVERT: B  369 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8773 (ptpp)
REVERT: C  305 SER cc_start: 0.8744 (p) cc_final: 0.8195 (p)
REVERT: C  307 GLN cc_start: 0.8748 (mt0) cc_final: 0.8358 (mp10)
REVERT: C  317 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7425 (ptpp)
REVERT: C  342 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8295 (mm-30)
REVERT: C  347 LYS cc_start: 0.8334 (tttt) cc_final: 0.8064 (mtpt)
REVERT: D  307 GLN cc_start: 0.9169 (mt0) cc_final: 0.8857 (tm-30)
REVERT: D  317 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7901 (ptpp)
REVERT: D  321 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8330 (mttp)
REVERT: D  342 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7944 (pm20)
REVERT: E  305 SER cc_start: 0.8822 (p) cc_final: 0.8476 (p)
REVERT: E  307 GLN cc_start: 0.8776 (mt0) cc_final: 0.8348 (tm-30)
REVERT: E  317 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7481 (ptpp)
REVERT: E  321 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8104 (mttp)
REVERT: E  342 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8352 (mm-30)
REVERT: E  347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8282 (mtpt)
REVERT: F  305 SER cc_start: 0.9146 (p) cc_final: 0.8702 (p)
REVERT: F  307 GLN cc_start: 0.9000 (mt0) cc_final: 0.8795 (mp10)
REVERT: F  317 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7972 (ptpp)
REVERT: F  338 GLU cc_start: 0.8259 (tt0) cc_final: 0.8020 (mt-10)
REVERT: F  342 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7993 (pm20)
REVERT: G  305 SER cc_start: 0.8590 (p) cc_final: 0.7920 (p)
REVERT: G  307 GLN cc_start: 0.8662 (mt0) cc_final: 0.8446 (mp10)
REVERT: G  317 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7710 (ptpp)
REVERT: G  369 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8604 (ptpp)
  outliers start: 21
  outliers final: 4
  residues processed: 135
  average time/residue: 0.2889
  time to fit residues: 44.2394
Evaluate side-chains
  68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
A 362 HIS
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
B 362 HIS
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 GLN
C 362 HIS
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 368 ASN
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN
E 362 HIS
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 351 GLN
G 362 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.108116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.089857 restraints weight = 6991.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 3.47
r_work: 0.3864 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4172  Z= 0.269
  Angle     :  0.699   7.937   5579  Z= 0.343
  Chirality :  0.049   0.127    623
  Planarity :  0.003   0.016    714
  Dihedral  :  5.652  16.792    557
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.22 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.17 (0.23), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.17), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 374 
 PHE   0.013   0.002   PHE E 378 
 TYR   0.007   0.002   TYR G 310 
 ARG   0.002   0.000   ARG E 349 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.7948 (mt0) cc_final: 0.7440 (tm-30)
REVERT: B  307 GLN cc_start: 0.8053 (mt0) cc_final: 0.7754 (mp10)
REVERT: B  342 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6756 (mm-30)
REVERT: D  342 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7562 (pm20)
REVERT: E  305 SER cc_start: 0.8864 (p) cc_final: 0.8583 (p)
REVERT: E  307 GLN cc_start: 0.8069 (mt0) cc_final: 0.7767 (tm-30)
REVERT: F  305 SER cc_start: 0.8894 (p) cc_final: 0.8191 (p)
REVERT: F  307 GLN cc_start: 0.8586 (mt0) cc_final: 0.8267 (mp10)
REVERT: F  338 GLU cc_start: 0.7895 (tt0) cc_final: 0.7598 (mt-10)
REVERT: F  342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7792 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 66
  average time/residue: 0.1491
  time to fit residues: 12.8345
Evaluate side-chains
  55 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 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 = 0.4293 r_free = 0.4293 target = 0.112480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.094118 restraints weight = 7324.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 3.45
r_work: 0.3845 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4172  Z= 0.280
  Angle     :  0.651   8.302   5579  Z= 0.321
  Chirality :  0.049   0.121    623
  Planarity :  0.003   0.015    714
  Dihedral  :  5.033  15.348    553
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.01 %
    Favored  : 85.71 %
  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: -3.61 (0.26), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.20), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 374 
 PHE   0.010   0.002   PHE E 378 
 TYR   0.006   0.002   TYR G 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  371 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8072 (mm)
REVERT: C  311 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8470 (mtpt)
REVERT: D  342 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7462 (pm20)
REVERT: E  307 GLN cc_start: 0.8000 (mt0) cc_final: 0.7679 (tm-30)
REVERT: E  347 LYS cc_start: 0.8056 (tttt) cc_final: 0.7594 (mttt)
REVERT: F  342 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7645 (pm20)
REVERT: G  307 GLN cc_start: 0.8273 (mt0) cc_final: 0.7926 (tm-30)
REVERT: G  344 LEU cc_start: 0.9050 (mp) cc_final: 0.8820 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 58
  average time/residue: 0.1826
  time to fit residues: 13.6631
Evaluate side-chains
  59 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  373 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    4.8988

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 HIS
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 HIS
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.100832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.083261 restraints weight = 7635.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 3.49
r_work: 0.3739 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   4172  Z= 0.450
  Angle     :  0.728   6.763   5579  Z= 0.371
  Chirality :  0.051   0.149    623
  Planarity :  0.003   0.021    714
  Dihedral  :  5.467  17.479    553
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 12.58 %
    Favored  : 83.80 %
  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: -3.61 (0.27), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.20), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS G 374 
 PHE   0.009   0.003   PHE E 378 
 TYR   0.005   0.002   TYR G 310 
 ARG   0.001   0.000   ARG E 349 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  371 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8110 (mm)
REVERT: B  307 GLN cc_start: 0.7591 (mp10) cc_final: 0.7130 (mp10)
REVERT: C  342 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: D  342 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7530 (pm20)
REVERT: E  307 GLN cc_start: 0.7924 (mt0) cc_final: 0.7698 (tm-30)
REVERT: F  342 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7682 (pm20)
REVERT: G  307 GLN cc_start: 0.8268 (mt0) cc_final: 0.7936 (tm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 68
  average time/residue: 0.1748
  time to fit residues: 15.0901
Evaluate side-chains
  66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 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 = 0.4178 r_free = 0.4178 target = 0.102761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.084937 restraints weight = 7666.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 3.55
r_work: 0.3771 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4172  Z= 0.321
  Angle     :  0.647   8.092   5579  Z= 0.322
  Chirality :  0.049   0.140    623
  Planarity :  0.002   0.014    714
  Dihedral  :  5.129  17.964    553
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 14.93 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.007   0.002   PHE E 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.001   0.000   ARG A 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: B  307 GLN cc_start: 0.7568 (mp10) cc_final: 0.7169 (mp10)
REVERT: B  342 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6825 (mm-30)
REVERT: D  342 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7518 (pm20)
REVERT: E  307 GLN cc_start: 0.7931 (mt0) cc_final: 0.7544 (mp10)
REVERT: F  342 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7674 (pm20)
REVERT: G  307 GLN cc_start: 0.8260 (mt0) cc_final: 0.7999 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1496
  time to fit residues: 12.5169
Evaluate side-chains
  66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain F residue  375 LYS
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  373 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0020
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.9996

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 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 = 0.4190 r_free = 0.4190 target = 0.103136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.085272 restraints weight = 7437.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 3.51
r_work: 0.3783 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4172  Z= 0.288
  Angle     :  0.629   7.846   5579  Z= 0.308
  Chirality :  0.048   0.119    623
  Planarity :  0.002   0.013    714
  Dihedral  :  4.957  16.811    553
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.57 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.006   0.002   PHE E 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: A  371 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mm)
REVERT: B  307 GLN cc_start: 0.7584 (mp10) cc_final: 0.7158 (mp10)
REVERT: B  342 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6822 (mm-30)
REVERT: D  342 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7570 (pm20)
REVERT: E  307 GLN cc_start: 0.7968 (mt0) cc_final: 0.7577 (mp10)
REVERT: F  342 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7934 (pm20)
REVERT: G  307 GLN cc_start: 0.8252 (mt0) cc_final: 0.7980 (mp10)
  outliers start: 16
  outliers final: 13
  residues processed: 66
  average time/residue: 0.1417
  time to fit residues: 12.3046
Evaluate side-chains
  71 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  373 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 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 = 0.4173 r_free = 0.4173 target = 0.102205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.084414 restraints weight = 7580.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 3.53
r_work: 0.3764 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4172  Z= 0.317
  Angle     :  0.640   9.330   5579  Z= 0.314
  Chirality :  0.048   0.119    623
  Planarity :  0.002   0.017    714
  Dihedral  :  4.980  17.094    553
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 15.78 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.006   0.002   PHE E 378 
 TYR   0.003   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7444 (mm-30)
REVERT: A  371 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (mm)
REVERT: B  307 GLN cc_start: 0.7586 (mp10) cc_final: 0.7170 (mp10)
REVERT: B  342 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6833 (mm-30)
REVERT: C  307 GLN cc_start: 0.8041 (mt0) cc_final: 0.7786 (mp10)
REVERT: D  342 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7587 (pm20)
REVERT: D  380 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6077 (tp30)
REVERT: E  307 GLN cc_start: 0.7973 (mt0) cc_final: 0.7630 (mp10)
REVERT: F  342 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7951 (pm20)
REVERT: G  307 GLN cc_start: 0.8261 (mt0) cc_final: 0.7901 (mp10)
  outliers start: 18
  outliers final: 16
  residues processed: 71
  average time/residue: 0.1515
  time to fit residues: 13.7910
Evaluate side-chains
  77 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  375 LYS
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  373 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 330 HIS
D 330 HIS
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.099936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.082284 restraints weight = 7630.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 3.49
r_work: 0.3724 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   4172  Z= 0.457
  Angle     :  0.724   9.641   5579  Z= 0.362
  Chirality :  0.050   0.119    623
  Planarity :  0.003   0.019    714
  Dihedral  :  5.421  18.421    553
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.57 %
    Favored  : 80.38 %
  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: -3.34 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 374 
 PHE   0.008   0.003   PHE E 378 
 TYR   0.003   0.001   TYR F 310 
 ARG   0.001   0.000   ARG E 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  371 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8168 (mm)
REVERT: B  307 GLN cc_start: 0.7525 (mp10) cc_final: 0.7302 (mp10)
REVERT: B  342 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6831 (mm-30)
REVERT: C  307 GLN cc_start: 0.8082 (mt0) cc_final: 0.7817 (mp10)
REVERT: D  342 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7547 (pm20)
REVERT: E  307 GLN cc_start: 0.8023 (mt0) cc_final: 0.7574 (mp10)
REVERT: F  342 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7962 (pm20)
REVERT: G  307 GLN cc_start: 0.8268 (mt0) cc_final: 0.8001 (mp10)
  outliers start: 19
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1387
  time to fit residues: 13.9082
Evaluate side-chains
  83 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  375 LYS
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  373 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0670
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0020
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.4130

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 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 = 0.4197 r_free = 0.4197 target = 0.104516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.086144 restraints weight = 7279.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 3.55
r_work: 0.3820 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4172  Z= 0.196
  Angle     :  0.664   9.809   5579  Z= 0.313
  Chirality :  0.048   0.122    623
  Planarity :  0.002   0.016    714
  Dihedral  :  4.688  14.749    553
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.55 %
    Favored  : 79.32 %
  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: -3.14 (0.30), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 374 
 PHE   0.005   0.001   PHE F 378 
 TYR   0.002   0.001   TYR G 310 
 ARG   0.001   0.000   ARG F 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7450 (mm-30)
REVERT: A  380 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6049 (tp30)
REVERT: B  307 GLN cc_start: 0.7678 (mp10) cc_final: 0.7257 (mp10)
REVERT: B  342 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6825 (mm-30)
REVERT: C  307 GLN cc_start: 0.8063 (mt0) cc_final: 0.7831 (mp10)
REVERT: D  342 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7577 (pm20)
REVERT: D  380 GLU cc_start: 0.6913 (tm-30) cc_final: 0.5844 (tp30)
REVERT: E  307 GLN cc_start: 0.7962 (mt0) cc_final: 0.7674 (mp10)
REVERT: F  342 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7680 (pm20)
REVERT: G  307 GLN cc_start: 0.8207 (mt0) cc_final: 0.7753 (mp10)
REVERT: G  380 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6444 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1440
  time to fit residues: 14.0246
Evaluate side-chains
  72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  373 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0060
   chunk 24 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6400

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
G 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.118305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.099035 restraints weight = 7060.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 3.65
r_work: 0.3920 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4172  Z= 0.152
  Angle     :  0.628   9.655   5579  Z= 0.290
  Chirality :  0.047   0.120    623
  Planarity :  0.002   0.020    714
  Dihedral  :  4.041  11.920    553
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 19.83 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.99 (0.30), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS C 374 
 PHE   0.003   0.001   PHE D 378 
 TYR   0.002   0.001   TYR E 310 
 ARG   0.000   0.000   ARG A 379 

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

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

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7433 (mm-30)
REVERT: A  347 LYS cc_start: 0.8103 (tttt) cc_final: 0.7673 (mttm)
REVERT: A  380 GLU cc_start: 0.6780 (tm-30) cc_final: 0.5962 (tp30)
REVERT: B  307 GLN cc_start: 0.7731 (mp10) cc_final: 0.7247 (mp10)
REVERT: B  342 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6775 (mm-30)
REVERT: B  380 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6679 (tp30)
REVERT: C  307 GLN cc_start: 0.8001 (mt0) cc_final: 0.7781 (mp10)
REVERT: D  342 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7593 (pm20)
REVERT: D  380 GLU cc_start: 0.6847 (tm-30) cc_final: 0.5798 (tp30)
REVERT: E  307 GLN cc_start: 0.7922 (mt0) cc_final: 0.7678 (mp10)
REVERT: E  356 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7862 (p)
REVERT: E  380 GLU cc_start: 0.6583 (tm-30) cc_final: 0.5782 (tp30)
REVERT: F  342 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7681 (pm20)
REVERT: F  380 GLU cc_start: 0.6619 (tm-30) cc_final: 0.5680 (tp30)
REVERT: G  307 GLN cc_start: 0.8248 (mt0) cc_final: 0.7753 (mp10)
REVERT: G  380 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6503 (tp30)
  outliers start: 5
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1569
  time to fit residues: 15.0194
Evaluate side-chains
  74 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 ASN
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.102884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.084713 restraints weight = 7337.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 3.50
r_work: 0.3797 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4172  Z= 0.292
  Angle     :  0.698   9.617   5579  Z= 0.330
  Chirality :  0.049   0.125    623
  Planarity :  0.002   0.019    714
  Dihedral  :  4.590  16.313    553
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.04 %
    Favored  : 78.46 %
  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: -3.02 (0.31), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.005   0.002   PHE E 378 
 TYR   0.003   0.001   TYR C 310 
 ARG   0.001   0.000   ARG B 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2380.96 seconds
wall clock time: 43 minutes 20.19 seconds (2600.19 seconds total)