Starting phenix.real_space_refine
on Wed Jun  4 15:33:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qjz_14027/06_2025/7qjz_14027.cif"
  }
  resolution = 3.4
  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       6      5.16       5
     C    2124      2.51       5
     N     612      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3378
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "D"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "E"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "F"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 563
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Time building chain proxies: 3.01, per 1000 atoms: 0.89
  Number of scatterers: 3378
  At special positions: 0
  Unit cell: (122.08, 116.63, 39.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     636      8.00
     N     612      7.00
     C    2124      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 444.2 milliseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 40.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 7.040A  pdb=" N   VAL A 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   VAL C 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.816A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 326 through 330
      removed outlier: 7.938A  pdb=" N   HIS C 330 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342
    Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 362
      removed outlier: 9.046A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 9.888A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   ASN B 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASP A 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   THR B 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE A 360 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLY A 355 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   SER C 356 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371
      removed outlier: 6.479A  pdb=" N   LYS A 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 306 through 310
      removed outlier: 6.461A  pdb=" N   GLN D 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   TYR E 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 316
      removed outlier: 7.341A  pdb=" N   SER E 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR D 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   CYS E 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LYS D 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 316
    Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 330
      removed outlier: 6.377A  pdb=" N   ASN D 327 " --> pdb=" O   ILE F 328 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   HIS F 330 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   HIS D 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 337 through 340
      removed outlier: 6.984A  pdb=" N   GLU D 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL D 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 362
      removed outlier: 8.960A  pdb=" N   VAL D 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   LYS E 353 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   SER D 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 10.417A  pdb=" N   GLY E 355 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   ILE D 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 9.975A  pdb=" N   LEU E 357 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER D 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ASN E 359 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   THR E 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE D 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 362
      removed outlier: 8.960A  pdb=" N   VAL D 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   LYS E 353 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   SER D 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 10.417A  pdb=" N   GLY E 355 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   ILE D 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 9.975A  pdb=" N   LEU E 357 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER D 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ASN E 359 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   THR E 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE D 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ILE F 354 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   GLY D 355 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER F 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 369 through 371
      removed outlier: 6.438A  pdb=" N   LYS D 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)

    51 hydrogen bonds defined for protein.
    153 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: 0.72

  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:
        1.21 -     1.33: 881
        1.33 -     1.45: 493
        1.45 -     1.57: 2052
        1.57 -     1.69: 0
        1.69 -     1.81: 6
  Bond restraints: 3432
  Sorted by residual:
  bond pdb=" CZ  ARG F 349 "
       pdb=" NH2 ARG F 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.03e+00
  bond pdb=" CA  LYS D 311 "
       pdb=" CB  LYS D 311 "
    ideal  model  delta    sigma   weight residual
    1.526  1.553 -0.026 9.30e-03 1.16e+04 8.02e+00
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.69e+00
  bond pdb=" CZ  ARG B 349 "
       pdb=" NH2 ARG B 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.45e+00
  bond pdb=" CZ  ARG E 349 "
       pdb=" NH2 ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.31e+00
  ... (remaining 3427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 3140
        2.01 -     4.03: 1170
        4.03 -     6.04: 261
        6.04 -     8.05: 21
        8.05 -    10.06: 4
  Bond angle restraints: 4596
  Sorted by residual:
  angle pdb=" CA  ASN C 327 "
        pdb=" CB  ASN C 327 "
        pdb=" CG  ASN C 327 "
      ideal   model   delta    sigma   weight residual
     112.60  119.73   -7.13 1.00e+00 1.00e+00 5.09e+01
  angle pdb=" CA  LYS C 331 "
        pdb=" C   LYS C 331 "
        pdb=" N   PRO C 332 "
      ideal   model   delta    sigma   weight residual
     118.16  122.99   -4.83 7.00e-01 2.04e+00 4.75e+01
  angle pdb=" CA  ASN A 327 "
        pdb=" CB  ASN A 327 "
        pdb=" CG  ASN A 327 "
      ideal   model   delta    sigma   weight residual
     112.60  119.09   -6.49 1.00e+00 1.00e+00 4.22e+01
  angle pdb=" CA  LYS B 331 "
        pdb=" C   LYS B 331 "
        pdb=" N   PRO B 332 "
      ideal   model   delta    sigma   weight residual
     118.16  122.34   -4.18 7.00e-01 2.04e+00 3.56e+01
  angle pdb=" CA  ASN B 327 "
        pdb=" CB  ASN B 327 "
        pdb=" CG  ASN B 327 "
      ideal   model   delta    sigma   weight residual
     112.60  118.20   -5.60 1.00e+00 1.00e+00 3.13e+01
  ... (remaining 4591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 1888
       16.24 -    32.48: 156
       32.48 -    48.72: 29
       48.72 -    64.96: 5
       64.96 -    81.19: 10
  Dihedral angle restraints: 2088
    sinusoidal: 864
      harmonic: 1224
  Sorted by residual:
  dihedral pdb=" CA  THR A 319 "
           pdb=" C   THR A 319 "
           pdb=" N   SER A 320 "
           pdb=" CA  SER A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.94   27.06     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  GLY F 365 "
           pdb=" C   GLY F 365 "
           pdb=" N   GLY F 366 "
           pdb=" CA  GLY F 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.00  -27.00     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  ASP E 314 "
           pdb=" C   ASP E 314 "
           pdb=" N   LEU E 315 "
           pdb=" CA  LEU E 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.52   26.48     0      5.00e+00 4.00e-02 2.80e+01
  ... (remaining 2085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 258
       0.062 -    0.124: 161
       0.124 -    0.185: 73
       0.185 -    0.247: 23
       0.247 -    0.309: 7
  Chirality restraints: 522
  Sorted by residual:
  chirality pdb=" CA  LYS C 343 "
            pdb=" N   LYS C 343 "
            pdb=" C   LYS C 343 "
            pdb=" CB  LYS C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  SER A 324 "
            pdb=" N   SER A 324 "
            pdb=" C   SER A 324 "
            pdb=" CB  SER A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  ASP D 345 "
            pdb=" N   ASP D 345 "
            pdb=" C   ASP D 345 "
            pdb=" CB  ASP D 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 519 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.075 2.00e-02 2.50e+03   5.14e-02 5.29e+01
        pdb=" CG  TYR E 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.097 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "    0.084 2.00e-02 2.50e+03   5.11e-02 5.22e+01
        pdb=" CG  TYR D 310 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "    0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F 329 "   -0.076 2.00e-02 2.50e+03   5.66e-02 4.81e+01
        pdb=" CG  HIS F 329 "    0.077 2.00e-02 2.50e+03
        pdb=" ND1 HIS F 329 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 HIS F 329 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 HIS F 329 "   -0.036 2.00e-02 2.50e+03
        pdb=" NE2 HIS F 329 "   -0.050 2.00e-02 2.50e+03
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1511
        2.97 -     3.45: 2933
        3.45 -     3.94: 5105
        3.94 -     4.42: 5246
        4.42 -     4.90: 10498
  Nonbonded interactions: 25293
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" OG  SER D 316 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" OG  SER F 316 "
     model   vdw
     2.539 3.040
  nonbonded pdb=" N   GLY A 366 "
            pdb=" O   GLY A 366 "
     model   vdw
     2.640 2.496
  nonbonded pdb=" OD2 ASP A 314 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.643 3.120
  ... (remaining 25288 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.820
  Find NCS groups from input model:        0.140
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
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      :  0.011   0.037   3432  Z= 0.730
  Angle     :  2.094  10.065   4596  Z= 1.374
  Chirality :  0.097   0.309    522
  Planarity :  0.013   0.062    582
  Dihedral  : 13.722  81.195   1308
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 0.44
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.32 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.30), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.004   HIS B 362 
 PHE   0.072   0.018   PHE E 346 
 TYR   0.097   0.028   TYR E 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16075 (   47)
  hydrogen bonds       : angle       7.19338 (  153)
  covalent geometry    : bond        0.01133 ( 3432)
  covalent geometry    : angle       2.09381 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 SER cc_start: 0.7637 (p) cc_final: 0.7416 (t)
REVERT: A  347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7784 (tptm)
REVERT: B  341 SER cc_start: 0.7599 (p) cc_final: 0.7306 (t)
REVERT: C  341 SER cc_start: 0.8039 (p) cc_final: 0.7824 (t)
REVERT: C  345 ASP cc_start: 0.8747 (t0) cc_final: 0.8365 (t0)
REVERT: C  347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7858 (tttt)
REVERT: C  353 LYS cc_start: 0.8249 (tttm) cc_final: 0.7741 (mtpt)
REVERT: E  321 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7755 (tptp)
REVERT: E  347 LYS cc_start: 0.7176 (mmtm) cc_final: 0.5849 (mtmm)
REVERT: F  343 LYS cc_start: 0.8540 (mtmt) cc_final: 0.6804 (tptt)
REVERT: F  349 ARG cc_start: 0.8927 (ttp80) cc_final: 0.7725 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2247
  time to fit residues: 23.6382
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
A 362 HIS
C 327 ASN
D 307 GLN
D 336 GLN
D 362 HIS
E 307 GLN
E 336 GLN
E 362 HIS
F 307 GLN
F 336 GLN
F 362 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.126980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.109261 restraints weight = 5214.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.43
r_work: 0.3803 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3432  Z= 0.261
  Angle     :  0.888   6.458   4596  Z= 0.461
  Chirality :  0.056   0.170    522
  Planarity :  0.005   0.031    582
  Dihedral  :  8.230  20.196    450
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 11.03 %
    Favored  : 87.95 %
  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: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS C 362 
 PHE   0.011   0.002   PHE D 346 
 TYR   0.021   0.006   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (   47)
  hydrogen bonds       : angle       6.23336 (  153)
  covalent geometry    : bond        0.00598 ( 3432)
  covalent geometry    : angle       0.88793 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7908 (mttt) cc_final: 0.7618 (tptm)
REVERT: A  353 LYS cc_start: 0.8286 (tttm) cc_final: 0.7441 (mtpt)
REVERT: A  375 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8013 (tttp)
REVERT: C  345 ASP cc_start: 0.8475 (t0) cc_final: 0.7745 (t0)
REVERT: C  347 LYS cc_start: 0.7696 (mttt) cc_final: 0.7320 (tttt)
REVERT: C  353 LYS cc_start: 0.8288 (tttm) cc_final: 0.7359 (mtpt)
REVERT: F  349 ARG cc_start: 0.8657 (ttp80) cc_final: 0.7302 (mmp80)
  outliers start: 4
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1915
  time to fit residues: 15.0170
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.0370
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.3264

-------------------------------------------------------------------------------
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 = 0.4221 r_free = 0.4221 target = 0.133297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.115421 restraints weight = 4964.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.41
r_work: 0.3899 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3432  Z= 0.115
  Angle     :  0.694   7.318   4596  Z= 0.351
  Chirality :  0.051   0.136    522
  Planarity :  0.003   0.026    582
  Dihedral  :  6.667  18.209    450
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.79 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS C 362 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.002   0.001   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02413 (   47)
  hydrogen bonds       : angle       5.88265 (  153)
  covalent geometry    : bond        0.00244 ( 3432)
  covalent geometry    : angle       0.69369 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7785 (mttt) cc_final: 0.7472 (tptm)
REVERT: A  353 LYS cc_start: 0.8213 (tttm) cc_final: 0.7534 (mtpt)
REVERT: A  363 VAL cc_start: 0.8984 (t) cc_final: 0.8763 (t)
REVERT: A  375 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7911 (tttp)
REVERT: B  307 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6772 (mp-120)
REVERT: B  347 LYS cc_start: 0.7727 (mttt) cc_final: 0.6916 (pttm)
REVERT: B  369 LYS cc_start: 0.8746 (tttp) cc_final: 0.7574 (mttt)
REVERT: C  345 ASP cc_start: 0.8538 (t0) cc_final: 0.7899 (t0)
REVERT: C  347 LYS cc_start: 0.7686 (mttt) cc_final: 0.7334 (tttt)
REVERT: C  353 LYS cc_start: 0.8242 (tttm) cc_final: 0.7378 (mtpt)
REVERT: C  369 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8319 (tttp)
REVERT: D  338 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7511 (tm-30)
REVERT: E  338 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: F  338 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: F  349 ARG cc_start: 0.8611 (ttp80) cc_final: 0.7575 (mmp80)
  outliers start: 7
  outliers final: 5
  residues processed: 69
  average time/residue: 0.1948
  time to fit residues: 15.8311
Evaluate side-chains
  66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  305 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 17 optimal weight:    0.0170
   chunk 33 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    5.0026

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

Flipped N/Q/H residues before XYZ refinement:
** B 368 ASN ** 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 = 0.4136 r_free = 0.4136 target = 0.126431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.108527 restraints weight = 5249.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.41
r_work: 0.3792 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3432  Z= 0.233
  Angle     :  0.757   5.541   4596  Z= 0.390
  Chirality :  0.052   0.137    522
  Planarity :  0.004   0.031    582
  Dihedral  :  6.698  17.897    450
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.85 %
    Favored  : 83.85 %
  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: -2.94 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS E 374 
 PHE   0.009   0.002   PHE D 346 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.005   0.001   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02575 (   47)
  hydrogen bonds       : angle       5.34573 (  153)
  covalent geometry    : bond        0.00529 ( 3432)
  covalent geometry    : angle       0.75655 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.7872 (mttt) cc_final: 0.7434 (tptm)
REVERT: A  353 LYS cc_start: 0.8319 (tttm) cc_final: 0.7384 (mtpt)
REVERT: A  375 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7705 (tttp)
REVERT: B  307 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7008 (mp10)
REVERT: B  347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7277 (pttm)
REVERT: C  307 GLN cc_start: 0.7509 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: C  347 LYS cc_start: 0.7647 (mttt) cc_final: 0.7287 (tttt)
REVERT: C  353 LYS cc_start: 0.8197 (tttm) cc_final: 0.7299 (mtpt)
REVERT: C  369 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8291 (tttp)
REVERT: C  375 LYS cc_start: 0.8386 (tttp) cc_final: 0.8074 (tttp)
REVERT: D  338 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: E  338 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: F  338 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: F  349 ARG cc_start: 0.8677 (ttp80) cc_final: 0.7576 (mmp80)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2095
  time to fit residues: 16.8372
Evaluate side-chains
  67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4187 r_free = 0.4187 target = 0.129377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.112365 restraints weight = 5128.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.25
r_work: 0.3825 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3432  Z= 0.246
  Angle     :  0.770   9.262   4596  Z= 0.394
  Chirality :  0.052   0.157    522
  Planarity :  0.004   0.026    582
  Dihedral  :  6.585  17.764    450
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.59 %
    Favored  : 83.33 %
  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: -3.03 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F 374 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02580 (   47)
  hydrogen bonds       : angle       5.49663 (  153)
  covalent geometry    : bond        0.00555 ( 3432)
  covalent geometry    : angle       0.76958 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.7932 (mttt) cc_final: 0.7614 (tttt)
REVERT: A  353 LYS cc_start: 0.8387 (tttm) cc_final: 0.7522 (mtpt)
REVERT: A  375 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7866 (tttp)
REVERT: B  307 GLN cc_start: 0.7492 (tm-30) cc_final: 0.7038 (mp-120)
REVERT: B  347 LYS cc_start: 0.8298 (mttt) cc_final: 0.7497 (pttm)
REVERT: B  369 LYS cc_start: 0.8949 (tttp) cc_final: 0.7669 (mttt)
REVERT: C  347 LYS cc_start: 0.7751 (mttt) cc_final: 0.7451 (tttt)
REVERT: C  369 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8071 (mttt)
REVERT: C  375 LYS cc_start: 0.8487 (tttp) cc_final: 0.8205 (tttp)
REVERT: D  338 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: D  349 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8668 (ttm-80)
REVERT: E  338 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: F  338 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7427 (tm-30)
REVERT: F  349 ARG cc_start: 0.8782 (ttp80) cc_final: 0.7709 (mmp80)
  outliers start: 12
  outliers final: 10
  residues processed: 66
  average time/residue: 0.2239
  time to fit residues: 17.3305
Evaluate side-chains
  67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4135 r_free = 0.4135 target = 0.125779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.108044 restraints weight = 5307.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.39
r_work: 0.3795 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3432  Z= 0.221
  Angle     :  0.748   8.560   4596  Z= 0.382
  Chirality :  0.052   0.164    522
  Planarity :  0.004   0.026    582
  Dihedral  :  6.380  17.396    450
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.62 %
    Favored  : 82.31 %
  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 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 362 
 PHE   0.012   0.002   PHE B 378 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.002   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02550 (   47)
  hydrogen bonds       : angle       5.28926 (  153)
  covalent geometry    : bond        0.00502 ( 3432)
  covalent geometry    : angle       0.74759 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8170 (mttp) cc_final: 0.7651 (mptt)
REVERT: A  347 LYS cc_start: 0.7899 (mttt) cc_final: 0.7568 (tttt)
REVERT: A  353 LYS cc_start: 0.8250 (tttm) cc_final: 0.7322 (mtpt)
REVERT: A  375 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7743 (tttp)
REVERT: B  307 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7146 (mp-120)
REVERT: B  347 LYS cc_start: 0.8317 (mttt) cc_final: 0.7476 (pttm)
REVERT: B  369 LYS cc_start: 0.8965 (tttp) cc_final: 0.7687 (mttt)
REVERT: C  307 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7303 (tm-30)
REVERT: C  347 LYS cc_start: 0.7796 (mttt) cc_final: 0.7521 (tttt)
REVERT: C  369 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7774 (mttt)
REVERT: C  371 ILE cc_start: 0.8485 (mp) cc_final: 0.8206 (mp)
REVERT: C  372 GLU cc_start: 0.7435 (mp0) cc_final: 0.7065 (mt-10)
REVERT: C  375 LYS cc_start: 0.8425 (tttp) cc_final: 0.8130 (tttp)
REVERT: D  338 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: E  338 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: F  338 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: F  349 ARG cc_start: 0.8788 (ttp80) cc_final: 0.7591 (mmp80)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1888
  time to fit residues: 15.7503
Evaluate side-chains
  69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.129687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.113150 restraints weight = 5063.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.14
r_work: 0.3852 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3432  Z= 0.211
  Angle     :  0.721   8.801   4596  Z= 0.368
  Chirality :  0.051   0.153    522
  Planarity :  0.003   0.028    582
  Dihedral  :  6.235  16.993    450
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.87 %
    Favored  : 81.79 %
  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 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 362 
 PHE   0.010   0.002   PHE B 378 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.001   0.000   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02479 (   47)
  hydrogen bonds       : angle       5.17737 (  153)
  covalent geometry    : bond        0.00477 ( 3432)
  covalent geometry    : angle       0.72112 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.8227 (mttp) cc_final: 0.7740 (mptt)
REVERT: A  347 LYS cc_start: 0.7790 (mttt) cc_final: 0.7590 (tttt)
REVERT: A  353 LYS cc_start: 0.8295 (tttm) cc_final: 0.7434 (mtpt)
REVERT: A  375 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7733 (tttp)
REVERT: B  307 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7293 (mp-120)
REVERT: B  347 LYS cc_start: 0.8370 (mttt) cc_final: 0.7522 (pttm)
REVERT: B  369 LYS cc_start: 0.8880 (tttp) cc_final: 0.7718 (mttt)
REVERT: C  347 LYS cc_start: 0.7895 (mttt) cc_final: 0.7613 (tttt)
REVERT: C  369 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7693 (mttt)
REVERT: C  372 GLU cc_start: 0.7441 (mp0) cc_final: 0.7080 (mp0)
REVERT: C  375 LYS cc_start: 0.8494 (tttp) cc_final: 0.8233 (tttp)
REVERT: D  338 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7586 (tm-30)
REVERT: E  338 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: F  338 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7444 (tm-30)
REVERT: F  349 ARG cc_start: 0.8789 (ttp80) cc_final: 0.7700 (mmp80)
  outliers start: 13
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1880
  time to fit residues: 15.4436
Evaluate side-chains
  68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0030
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1998

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4250 r_free = 0.4250 target = 0.134693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.117779 restraints weight = 4954.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 2.26
r_work: 0.3903 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3432  Z= 0.123
  Angle     :  0.650   9.321   4596  Z= 0.328
  Chirality :  0.050   0.161    522
  Planarity :  0.003   0.030    582
  Dihedral  :  5.768  15.654    450
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.13 %
    Favored  : 82.56 %
  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: -2.83 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B 362 
 PHE   0.006   0.001   PHE D 346 
 TYR   0.005   0.001   TYR B 310 
 ARG   0.001   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02181 (   47)
  hydrogen bonds       : angle       4.94213 (  153)
  covalent geometry    : bond        0.00278 ( 3432)
  covalent geometry    : angle       0.65019 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8248 (tttm) cc_final: 0.7411 (mtpt)
REVERT: A  375 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7964 (tttp)
REVERT: B  347 LYS cc_start: 0.8319 (mttt) cc_final: 0.7491 (pttm)
REVERT: B  369 LYS cc_start: 0.8820 (tttp) cc_final: 0.7696 (mttt)
REVERT: B  375 LYS cc_start: 0.4965 (OUTLIER) cc_final: 0.3367 (tptm)
REVERT: C  307 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7184 (tm-30)
REVERT: C  321 LYS cc_start: 0.7813 (mttt) cc_final: 0.7331 (mttp)
REVERT: C  347 LYS cc_start: 0.8042 (mttt) cc_final: 0.7803 (tttt)
REVERT: C  369 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7789 (mttt)
REVERT: D  338 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: F  338 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7197 (tm-30)
REVERT: F  349 ARG cc_start: 0.8798 (ttp80) cc_final: 0.7696 (mmp80)
  outliers start: 9
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1995
  time to fit residues: 16.0508
Evaluate side-chains
  68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:   30.0000
   chunk 39 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0010
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.0590

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4263 r_free = 0.4263 target = 0.135289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.118244 restraints weight = 4830.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 2.17
r_work: 0.3926 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3834 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3432  Z= 0.119
  Angle     :  0.643   9.036   4596  Z= 0.323
  Chirality :  0.050   0.153    522
  Planarity :  0.003   0.035    582
  Dihedral  :  5.533  14.169    450
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.13 %
    Favored  : 82.05 %
  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: -2.74 (0.35), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 362 
 PHE   0.018   0.001   PHE B 346 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02108 (   47)
  hydrogen bonds       : angle       4.79875 (  153)
  covalent geometry    : bond        0.00268 ( 3432)
  covalent geometry    : angle       0.64265 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8228 (tttm) cc_final: 0.7403 (mtpt)
REVERT: A  375 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7914 (tttp)
REVERT: B  347 LYS cc_start: 0.8179 (mttt) cc_final: 0.7426 (pttm)
REVERT: B  369 LYS cc_start: 0.8799 (tttp) cc_final: 0.7706 (mttt)
REVERT: B  375 LYS cc_start: 0.5082 (OUTLIER) cc_final: 0.3427 (tptm)
REVERT: C  307 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: C  321 LYS cc_start: 0.7815 (mttt) cc_final: 0.7332 (mttp)
REVERT: C  347 LYS cc_start: 0.8036 (mttt) cc_final: 0.7835 (tttt)
REVERT: C  353 LYS cc_start: 0.8012 (tttm) cc_final: 0.7373 (mtpt)
REVERT: C  369 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7886 (mttt)
REVERT: D  338 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: F  338 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: F  349 ARG cc_start: 0.8765 (ttp80) cc_final: 0.7679 (mmp80)
  outliers start: 11
  outliers final: 5
  residues processed: 65
  average time/residue: 0.2041
  time to fit residues: 15.6582
Evaluate side-chains
  63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain F residue  371 ILE
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4211 r_free = 0.4211 target = 0.130848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.113705 restraints weight = 5014.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.25
r_work: 0.3854 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3432  Z= 0.200
  Angle     :  0.711   8.304   4596  Z= 0.362
  Chirality :  0.051   0.159    522
  Planarity :  0.004   0.040    582
  Dihedral  :  5.840  14.931    450
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.64 %
    Favored  : 82.05 %
  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 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 362 
 PHE   0.015   0.002   PHE B 346 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02456 (   47)
  hydrogen bonds       : angle       4.86889 (  153)
  covalent geometry    : bond        0.00453 ( 3432)
  covalent geometry    : angle       0.71111 ( 4596)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8324 (tttm) cc_final: 0.7406 (mtpt)
REVERT: A  375 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7937 (tttp)
REVERT: B  347 LYS cc_start: 0.8279 (mttt) cc_final: 0.7460 (mtmm)
REVERT: B  369 LYS cc_start: 0.8867 (tttp) cc_final: 0.7710 (mttt)
REVERT: B  375 LYS cc_start: 0.4695 (OUTLIER) cc_final: 0.3133 (tptm)
REVERT: C  307 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: C  321 LYS cc_start: 0.7866 (mttt) cc_final: 0.7376 (mttp)
REVERT: C  353 LYS cc_start: 0.8050 (tttm) cc_final: 0.7347 (mtpp)
REVERT: C  369 LYS cc_start: 0.8527 (ttpt) cc_final: 0.7903 (mttt)
REVERT: D  338 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: F  338 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7264 (tm-30)
REVERT: F  349 ARG cc_start: 0.8810 (ttp80) cc_final: 0.7723 (mmp80)
  outliers start: 9
  outliers final: 6
  residues processed: 61
  average time/residue: 0.2045
  time to fit residues: 14.7795
Evaluate side-chains
  61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  371 ILE
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  376 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0010
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    3.7792

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 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 = 0.4213 r_free = 0.4213 target = 0.131222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.114341 restraints weight = 5077.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.20
r_work: 0.3862 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3432  Z= 0.178
  Angle     :  0.706   8.548   4596  Z= 0.359
  Chirality :  0.051   0.153    522
  Planarity :  0.004   0.038    582
  Dihedral  :  5.849  14.986    450
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.15 %
    Favored  : 81.79 %
  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: -2.97 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 362 
 PHE   0.016   0.002   PHE B 346 
 TYR   0.005   0.002   TYR B 310 
 ARG   0.002   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02258 (   47)
  hydrogen bonds       : angle       4.84680 (  153)
  covalent geometry    : bond        0.00408 ( 3432)
  covalent geometry    : angle       0.70588 ( 4596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2144.32 seconds
wall clock time: 37 minutes 48.48 seconds (2268.48 seconds total)