Starting phenix.real_space_refine
on Fri Mar 14 02:42:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hco_34660/03_2025/8hco_34660_neut.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 69 atoms to isotropic.
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      29      5.16       5
     C    5966      2.51       5
     N    1568      2.21       5
     O    1767      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9330
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2507
          Classifications: {'peptide': 326}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 314}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "C"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "E"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 295
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 4, 'TRANS': 31}
    Chain: "G"
      Number of atoms: 458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 458
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 4, 'TRANS': 56}
    Chain: "G"
      Number of atoms: 1333
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 163, 1332
          Unusual residues: {'GYS': 1}
          Classifications: {'peptide': 162, 'undetermined': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1}
            Not linked:
              pdbres="GYS G 344 "
              pdbres="VAL G 346 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'GYS:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 163, 1332
          Unusual residues: {'GYS': 1}
          Classifications: {'peptide': 162, 'undetermined': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1}
            Not linked:
              pdbres="GYS G 344 "
              pdbres="VAL G 346 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'GYS:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 1361
    Chain: "I"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2528
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "K"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "L"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "M"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 295
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 4, 'TRANS': 31}
  Time building chain proxies: 7.27, per 1000 atoms: 0.78
  Number of scatterers: 9330
  At special positions: 0
  Unit cell: (98.44, 133.75, 120.91, 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      29     16.00
     O    1767      8.00
     N    1568      7.00
     C    5966      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 additional links: simple=2, symmetry=0
    Simple link:   pdb=" C   GYS G 344 " - pdb=" N   VAL G 346 "
    Simple link:   pdb=" C   PHE G 342 " - pdb=" N   GYS G 344 "
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.08
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2212

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      26.0% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 56
      removed outlier: 4.378A  pdb=" N   GLN A  53 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.672A  pdb=" N   GLN A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 135
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'C' and resid 14 through 48
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'D' and resid 30 through 50
    Processing helix  chain 'D' and resid 51 through 58
      removed outlier: 3.588A  pdb=" N   ASP D  55 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 42
      removed outlier: 3.848A  pdb=" N   TRP E  32 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ILE E  33 " --> pdb=" O   HIS E  29 " (cutoff:3.500A)
      Proline residue:  E  34  - end of helix
    Processing helix  chain 'E' and resid 49 through 55
    Processing helix  chain 'G' and resid 334 through 340
      removed outlier: 4.840A  pdb=" N   THR G 340 " --> pdb=" O   PRO G 336 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 364 through 372
      removed outlier: 3.651A  pdb=" N   GLN I 372 " --> pdb=" O   LEU I 368 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 87 through 135
      Proline residue:  J 112  - end of helix
    Processing helix  chain 'K' and resid 14 through 48
      Proline residue:  K  39  - end of helix
    Processing helix  chain 'L' and resid 30 through 50
    Processing helix  chain 'L' and resid 51 through 58
      removed outlier: 3.786A  pdb=" N   ASP L  55 " --> pdb=" O   SER L  51 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 31 through 43
      removed outlier: 3.552A  pdb=" N   PHE M  35 " --> pdb=" O   GLY M  31 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS M  43 " --> pdb=" O   LEU M  39 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 49 through 55
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 93
      removed outlier: 6.067A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   CYS A 165 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   THR A 194 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A 255 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 275 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ASP A 319 " --> pdb=" O   LYS A 323 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LYS A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 290 through 300
      removed outlier: 3.604A  pdb=" N   VAL G 290 " --> pdb=" O   GLY G 313 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY G 313 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL G 294 " --> pdb=" O   GLY G 309 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY G 309 " --> pdb=" O   VAL G 294 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU G 296 " --> pdb=" O   VAL G 307 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL G 307 " --> pdb=" O   LEU G 296 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY G 298 " --> pdb=" O   PHE G 305 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE G 305 " --> pdb=" O   GLY G 298 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG G 308 " --> pdb=" O   ILE G 325 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS G 323 " --> pdb=" O   GLU G 310 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL G 497 " --> pdb=" O   SER G 486 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER G 486 " --> pdb=" O   VAL G 497 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR G 478 " --> pdb=" O   ALA G 505 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ASN G 427 " --> pdb=" O   LYS G 444 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LYS G 444 " --> pdb=" O   ASN G 427 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR G 429 " --> pdb=" O   ASN G 442 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE G 439 " --> pdb=" O   ASN G 463 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE G 443 " --> pdb=" O   HIS G 459 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA G 457 " --> pdb=" O   ILE G 445 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS G 447 " --> pdb=" O   GLN G 455 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP G 458 " --> pdb=" O   SER G 377 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE G 406 " --> pdb=" O   THR G 383 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS G 391 " --> pdb=" O   VAL G 398 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   ASN G 399 " --> pdb=" O   PRO G 291 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU G 293 " --> pdb=" O   ASN G 399 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   ILE G 401 " --> pdb=" O   LEU G 293 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   GLU G 295 " --> pdb=" O   ILE G 401 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU G 403 " --> pdb=" O   GLU G 295 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ASP G 297 " --> pdb=" O   LEU G 403 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   GLY G 405 " --> pdb=" O   ASP G 297 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP G 299 " --> pdb=" O   GLY G 405 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 85 through 91
      removed outlier: 3.773A  pdb=" N   ALA I 257 " --> pdb=" O   THR I 273 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 279 through 281

    549 hydrogen bonds defined for protein.
    1584 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: 2.86

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1874
        1.33 -     1.45: 2305
        1.45 -     1.57: 5309
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 9537
  Sorted by residual:
  bond pdb=" CB1 GYS G 344 "
       pdb=" OG1BGYS G 344 "
    ideal  model  delta    sigma   weight residual
    1.408  1.611 -0.203 2.00e-02 2.50e+03 1.04e+02
  bond pdb=" N   VAL G 339 "
       pdb=" CA  VAL G 339 "
    ideal  model  delta    sigma   weight residual
    1.461  1.503 -0.042 1.17e-02 7.31e+03 1.26e+01
  bond pdb=" N   THR G 340 "
       pdb=" CA  THR G 340 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.05e+01
  bond pdb=" N   MET G 366 "
       pdb=" CA  MET G 366 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.04e-02 9.25e+03 1.03e+01
  bond pdb=" N   ASN I  95 "
       pdb=" CA  ASN I  95 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.20e-03 1.18e+04 9.94e+00
  ... (remaining 9532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 12595
        2.55 -     5.10: 295
        5.10 -     7.65: 36
        7.65 -    10.20: 10
       10.20 -    12.75: 2
  Bond angle restraints: 12938
  Sorted by residual:
  angle pdb=" N   VAL G 339 "
        pdb=" CA  VAL G 339 "
        pdb=" C   VAL G 339 "
      ideal   model   delta    sigma   weight residual
     110.42  116.05   -5.63 9.60e-01 1.09e+00 3.44e+01
  angle pdb=" C   LYS G 436 "
        pdb=" N   ASN G 437 "
        pdb=" CA  ASN G 437 "
      ideal   model   delta    sigma   weight residual
     121.54  131.47   -9.93 1.91e+00 2.74e-01 2.70e+01
  angle pdb=" N   PRO I  96 "
        pdb=" CA  PRO I  96 "
        pdb=" C   PRO I  96 "
      ideal   model   delta    sigma   weight residual
     112.47  102.27   10.20 2.06e+00 2.36e-01 2.45e+01
  angle pdb=" C   ASN A 133 "
        pdb=" N   ASP A 134 "
        pdb=" CA  ASP A 134 "
      ideal   model   delta    sigma   weight residual
     121.54  130.26   -8.72 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" CA  VAL G 339 "
        pdb=" C   VAL G 339 "
        pdb=" O   VAL G 339 "
      ideal   model   delta    sigma   weight residual
     121.17  116.63    4.54 1.06e+00 8.90e-01 1.84e+01
  ... (remaining 12933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5007
       17.86 -    35.73: 448
       35.73 -    53.59: 124
       53.59 -    71.45: 35
       71.45 -    89.31: 5
  Dihedral angle restraints: 5619
    sinusoidal: 2192
      harmonic: 3427
  Sorted by residual:
  dihedral pdb=" CA  THR G 316 "
           pdb=" C   THR G 316 "
           pdb=" N   ASN G 317 "
           pdb=" CA  ASN G 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ASN A  95 "
           pdb=" C   ASN A  95 "
           pdb=" N   PRO A  96 "
           pdb=" CA  PRO A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.97   23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  ASN A 133 "
           pdb=" C   ASN A 133 "
           pdb=" N   ASP A 134 "
           pdb=" CA  ASP A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.42  -20.58     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1081
       0.058 -    0.117: 274
       0.117 -    0.175: 76
       0.175 -    0.233: 14
       0.233 -    0.292: 5
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CB  ILE I 106 "
            pdb=" CA  ILE I 106 "
            pdb=" CG1 ILE I 106 "
            pdb=" CG2 ILE I 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE I 150 "
            pdb=" CA  ILE I 150 "
            pdb=" CG1 ILE I 150 "
            pdb=" CG2 ILE I 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  PHE I  98 "
            pdb=" N   PHE I  98 "
            pdb=" C   PHE I  98 "
            pdb=" CB  PHE I  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1447 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 GYS G 344 "   -0.013 2.00e-02 2.50e+03   8.89e-02 1.97e+02
        pdb=" CG2 GYS G 344 "   -0.141 2.00e-02 2.50e+03
        pdb=" C1  GYS G 344 "    0.043 2.00e-02 2.50e+03
        pdb=" C2  GYS G 344 "    0.065 2.00e-02 2.50e+03
        pdb=" CA1 GYS G 344 "   -0.024 2.00e-02 2.50e+03
        pdb=" CA2 GYS G 344 "    0.088 2.00e-02 2.50e+03
        pdb=" CA3 GYS G 344 "   -0.186 2.00e-02 2.50e+03
        pdb=" N2  GYS G 344 "    0.072 2.00e-02 2.50e+03
        pdb=" N3  GYS G 344 "    0.055 2.00e-02 2.50e+03
        pdb=" O2  GYS G 344 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G 337 "    0.024 2.00e-02 2.50e+03   4.88e-02 2.38e+01
        pdb=" C   THR G 337 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   THR G 337 "    0.031 2.00e-02 2.50e+03
        pdb=" N   LEU G 338 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 GYS G 344 "    0.028 2.00e-02 2.50e+03   2.40e-02 1.15e+01
        pdb=" CG2 GYS G 344 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 GYS G 344 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 GYS G 344 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 GYS G 344 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 GYS G 344 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  GYS G 344 "   -0.023 2.00e-02 2.50e+03
        pdb=" OH  GYS G 344 "    0.046 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2538
        2.81 -     3.33: 7157
        3.33 -     3.86: 15881
        3.86 -     4.38: 16820
        4.38 -     4.90: 30151
  Nonbonded interactions: 72547
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G 383 "
            pdb=" NZ  LYS G 385 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ALA B  99 "
            pdb=" OG1 THR B 103 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" O   ALA J  99 "
            pdb=" OG1 THR J 103 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OG  SER A 238 "
            pdb=" O   TRP A 243 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   GLN C  20 "
            pdb=" OG1 THR C  24 "
     model   vdw
     2.380 3.040
  ... (remaining 72542 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'I' and (resid 49 through 282 or resid 291 through 382))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'M'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     26.670
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
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      :  0.007   0.203   9537  Z= 0.425
  Angle     :  0.965  12.753  12938  Z= 0.561
  Chirality :  0.060   0.292   1450
  Planarity :  0.008   0.089   1667
  Dihedral  : 15.439  89.313   3405
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers : 10.99 %
    Allowed  : 13.76 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.21), residues: 1166
  helix: -2.53 (0.18), residues: 308
  sheet: -0.53 (0.22), residues: 479
  loop : -1.83 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K  42 
 HIS   0.004   0.001   HIS M  29 
 PHE   0.028   0.003   PHE G 342 
 TYR   0.014   0.002   TYR M  30 
 ARG   0.003   0.000   ARG A 315 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 383
  time to evaluate  : 1.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7142 (ttm-80)
REVERT: A   69 GLU cc_start: 0.8313 (mp0) cc_final: 0.7725 (mp0)
REVERT: A  120 PHE cc_start: 0.8599 (t80) cc_final: 0.8358 (t80)
REVERT: A  132 ASP cc_start: 0.8517 (m-30) cc_final: 0.8210 (m-30)
REVERT: A  169 GLN cc_start: 0.7818 (mt0) cc_final: 0.7413 (mt0)
REVERT: A  183 LEU cc_start: 0.8856 (tp) cc_final: 0.8499 (tp)
REVERT: A  184 ASN cc_start: 0.8548 (m-40) cc_final: 0.8153 (m110)
REVERT: A  203 GLN cc_start: 0.7945 (tt0) cc_final: 0.7105 (tt0)
REVERT: A  235 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8132 (ttt180)
REVERT: A  240 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7798 (ttpt)
REVERT: A  249 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8694 (mp)
REVERT: A  250 GLN cc_start: 0.7998 (mm110) cc_final: 0.7696 (tp40)
REVERT: A  314 TYR cc_start: 0.8950 (t80) cc_final: 0.8205 (t80)
REVERT: A  336 LEU cc_start: 0.8848 (tp) cc_final: 0.8575 (tt)
REVERT: A  349 ASN cc_start: 0.8280 (m110) cc_final: 0.7971 (t0)
REVERT: A  369 MET cc_start: 0.7713 (mmm) cc_final: 0.7375 (mmm)
REVERT: B  122 GLN cc_start: 0.8078 (tt0) cc_final: 0.7865 (tp40)
REVERT: D   54 MET cc_start: 0.8329 (tpt) cc_final: 0.7844 (tpp)
REVERT: D   56 MET cc_start: 0.6597 (mtt) cc_final: 0.6152 (mtt)
REVERT: E   49 ASN cc_start: 0.8443 (p0) cc_final: 0.7802 (p0)
REVERT: E   52 ASN cc_start: 0.8864 (t0) cc_final: 0.8425 (t0)
REVERT: G  300 VAL cc_start: 0.5146 (OUTLIER) cc_final: 0.4757 (m)
REVERT: G  338 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1798 (mp)
REVERT: G  397 LEU cc_start: -0.0330 (OUTLIER) cc_final: -0.0620 (tm)
REVERT: G  398 VAL cc_start: 0.2215 (t) cc_final: 0.1997 (t)
REVERT: G  447 HIS cc_start: 0.3455 (OUTLIER) cc_final: 0.1646 (m-70)
REVERT: I   74 VAL cc_start: 0.9295 (t) cc_final: 0.8932 (m)
REVERT: I   75 PHE cc_start: 0.8939 (m-80) cc_final: 0.8566 (m-80)
REVERT: I   79 TYR cc_start: 0.8508 (m-80) cc_final: 0.8013 (m-10)
REVERT: I   94 MET cc_start: 0.6299 (tpt) cc_final: 0.5888 (tmm)
REVERT: I  120 PHE cc_start: 0.8463 (t80) cc_final: 0.8010 (t80)
REVERT: I  140 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (ttp-110)
REVERT: I  143 TYR cc_start: 0.8661 (t80) cc_final: 0.7905 (t80)
REVERT: I  179 ASN cc_start: 0.7816 (t0) cc_final: 0.7509 (t0)
REVERT: I  181 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8871 (ptmt)
REVERT: I  183 LEU cc_start: 0.8940 (tp) cc_final: 0.8588 (tp)
REVERT: I  184 ASN cc_start: 0.9088 (m-40) cc_final: 0.8708 (m-40)
REVERT: I  187 PHE cc_start: 0.7021 (m-80) cc_final: 0.5501 (p90)
REVERT: I  198 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8806 (t)
REVERT: I  211 LEU cc_start: 0.9050 (tp) cc_final: 0.8835 (mm)
REVERT: I  227 ASP cc_start: 0.8182 (m-30) cc_final: 0.7500 (t0)
REVERT: I  297 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (p)
REVERT: I  310 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7360 (ptm-80)
REVERT: I  324 VAL cc_start: 0.9259 (t) cc_final: 0.9018 (p)
REVERT: I  359 PHE cc_start: 0.8440 (t80) cc_final: 0.8126 (t80)
REVERT: I  375 ASP cc_start: 0.7520 (t0) cc_final: 0.6698 (t0)
REVERT: J   89 ARG cc_start: 0.5330 (tpt90) cc_final: 0.3900 (mtt90)
REVERT: K   18 GLN cc_start: 0.8250 (tt0) cc_final: 0.7930 (pt0)
REVERT: K   22 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7383 (mt-10)
REVERT: K   30 TYR cc_start: 0.6043 (m-10) cc_final: 0.5832 (t80)
REVERT: L   55 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7474 (m-30)
REVERT: L   56 MET cc_start: 0.6355 (mtt) cc_final: 0.5766 (mtp)
REVERT: M   32 TRP cc_start: 0.8257 (t-100) cc_final: 0.7847 (t-100)
REVERT: M   35 PHE cc_start: 0.8328 (t80) cc_final: 0.7812 (t80)
REVERT: M   49 ASN cc_start: 0.8231 (p0) cc_final: 0.7538 (p0)
  outliers start: 111
  outliers final: 29
  residues processed: 443
  average time/residue: 0.2474
  time to fit residues: 153.0740
Evaluate side-chains
  314 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 276
  time to evaluate  : 1.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.3980
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0270
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    0.3980
   chunk 66 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 317 ASN
I  67 ASN
I  89 ASN
** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 ASN
M  52 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.170720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127996 restraints weight = 16333.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128942 restraints weight = 8811.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130733 restraints weight = 6143.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9537  Z= 0.182
  Angle     :  0.637   6.929  12938  Z= 0.327
  Chirality :  0.044   0.180   1450
  Planarity :  0.005   0.052   1667
  Dihedral  :  4.783  40.599   1252
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  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: -1.09 (0.23), residues: 1166
  helix:  0.01 (0.26), residues: 300
  sheet: -0.52 (0.22), residues: 494
  loop : -1.37 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 243 
 HIS   0.005   0.001   HIS G 355 
 PHE   0.013   0.001   PHE I 359 
 TYR   0.014   0.001   TYR G 478 
 ARG   0.005   0.001   ARG A 219 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 346
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.9611 (mm) cc_final: 0.9314 (mm)
REVERT: A  169 GLN cc_start: 0.7795 (mt0) cc_final: 0.7352 (mt0)
REVERT: A  219 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7554 (tpp80)
REVERT: A  240 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7600 (ttpt)
REVERT: A  244 ILE cc_start: 0.9330 (pt) cc_final: 0.8836 (pt)
REVERT: A  259 LEU cc_start: 0.9275 (tp) cc_final: 0.8938 (tp)
REVERT: A  298 GLU cc_start: 0.8710 (tp30) cc_final: 0.8497 (tp30)
REVERT: A  314 TYR cc_start: 0.8762 (t80) cc_final: 0.8144 (t80)
REVERT: A  336 LEU cc_start: 0.8906 (tp) cc_final: 0.8594 (tt)
REVERT: A  349 ASN cc_start: 0.8396 (m110) cc_final: 0.8089 (t0)
REVERT: A  369 MET cc_start: 0.7851 (mmm) cc_final: 0.7548 (mmm)
REVERT: C   20 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7210 (tp-100)
REVERT: C   23 LYS cc_start: 0.8967 (mttt) cc_final: 0.8534 (mppt)
REVERT: C   24 THR cc_start: 0.9319 (m) cc_final: 0.8580 (m)
REVERT: E   49 ASN cc_start: 0.8369 (p0) cc_final: 0.7819 (p0)
REVERT: G  366 MET cc_start: 0.0879 (mmm) cc_final: 0.0088 (mtt)
REVERT: I   94 MET cc_start: 0.6509 (tpt) cc_final: 0.6166 (tmm)
REVERT: I  150 ILE cc_start: 0.9278 (tp) cc_final: 0.8986 (mt)
REVERT: I  179 ASN cc_start: 0.8262 (t0) cc_final: 0.7955 (t0)
REVERT: I  181 LYS cc_start: 0.9179 (ptpp) cc_final: 0.8815 (ptmt)
REVERT: I  227 ASP cc_start: 0.8440 (m-30) cc_final: 0.7965 (t0)
REVERT: I  234 THR cc_start: 0.9195 (m) cc_final: 0.8922 (p)
REVERT: I  310 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7406 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8541 (t80) cc_final: 0.8262 (t80)
REVERT: J   89 ARG cc_start: 0.5622 (tpt90) cc_final: 0.3993 (mtt90)
REVERT: J  102 LEU cc_start: 0.8940 (tp) cc_final: 0.8730 (tp)
REVERT: J  113 LEU cc_start: 0.8807 (tp) cc_final: 0.8588 (tp)
REVERT: J  121 GLN cc_start: 0.7566 (mm110) cc_final: 0.7016 (mt0)
REVERT: K   22 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7479 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 346
  average time/residue: 0.1844
  time to fit residues: 91.1818
Evaluate side-chains
  280 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 279
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  38 ASN
M  29 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.168044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127082 restraints weight = 16567.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.126510 restraints weight = 9937.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127473 restraints weight = 7301.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9537  Z= 0.203
  Angle     :  0.601   7.656  12938  Z= 0.312
  Chirality :  0.043   0.185   1450
  Planarity :  0.004   0.040   1667
  Dihedral  :  4.532  33.086   1252
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  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: -0.45 (0.24), residues: 1166
  helix:  1.05 (0.28), residues: 299
  sheet: -0.49 (0.23), residues: 497
  loop : -0.91 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 243 
 HIS   0.007   0.001   HIS A 102 
 PHE   0.020   0.002   PHE I 120 
 TYR   0.021   0.001   TYR A 307 
 ARG   0.005   0.000   ARG A 315 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 323
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.8298 (tp40) cc_final: 0.8012 (tp40)
REVERT: A  169 GLN cc_start: 0.7684 (mt0) cc_final: 0.7321 (mt0)
REVERT: A  219 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7084 (tpp80)
REVERT: A  240 LYS cc_start: 0.7798 (ptpt) cc_final: 0.7569 (ttpt)
REVERT: A  259 LEU cc_start: 0.9277 (tp) cc_final: 0.8981 (tp)
REVERT: A  314 TYR cc_start: 0.8770 (t80) cc_final: 0.8051 (t80)
REVERT: A  323 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8317 (mtmm)
REVERT: A  349 ASN cc_start: 0.8342 (m110) cc_final: 0.8101 (t0)
REVERT: A  357 LEU cc_start: 0.9339 (pt) cc_final: 0.9070 (pt)
REVERT: A  369 MET cc_start: 0.7743 (mmm) cc_final: 0.7519 (mmm)
REVERT: C   23 LYS cc_start: 0.8935 (mttt) cc_final: 0.8690 (mttm)
REVERT: C   40 MET cc_start: 0.8527 (mpp) cc_final: 0.8325 (mpp)
REVERT: E   49 ASN cc_start: 0.8302 (p0) cc_final: 0.7839 (p0)
REVERT: G  397 LEU cc_start: 0.3822 (tp) cc_final: 0.3240 (pt)
REVERT: G  496 MET cc_start: -0.0026 (mpp) cc_final: -0.0722 (mtp)
REVERT: I  120 PHE cc_start: 0.8604 (t80) cc_final: 0.8349 (t80)
REVERT: I  132 ASP cc_start: 0.8017 (m-30) cc_final: 0.7815 (m-30)
REVERT: I  170 ASP cc_start: 0.7865 (t0) cc_final: 0.7653 (t0)
REVERT: I  179 ASN cc_start: 0.8226 (t0) cc_final: 0.7743 (t0)
REVERT: I  181 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8839 (ptmt)
REVERT: I  203 GLN cc_start: 0.7672 (tt0) cc_final: 0.7116 (tp40)
REVERT: I  227 ASP cc_start: 0.8326 (m-30) cc_final: 0.7932 (t0)
REVERT: I  310 ARG cc_start: 0.7841 (ptp90) cc_final: 0.7426 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8466 (t80) cc_final: 0.7973 (t80)
REVERT: J   87 PHE cc_start: 0.3928 (t80) cc_final: 0.3718 (t80)
REVERT: J   89 ARG cc_start: 0.5820 (tpt90) cc_final: 0.4098 (mtt90)
REVERT: J  113 LEU cc_start: 0.8876 (tp) cc_final: 0.8648 (tp)
REVERT: J  121 GLN cc_start: 0.7642 (mm110) cc_final: 0.7131 (mt0)
REVERT: K   22 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7430 (mt-10)
REVERT: M   52 ASN cc_start: 0.8508 (m-40) cc_final: 0.8268 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 323
  average time/residue: 0.1893
  time to fit residues: 87.0474
Evaluate side-chains
  273 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 65 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.168250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.124579 restraints weight = 16471.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.124974 restraints weight = 10238.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126279 restraints weight = 7355.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9537  Z= 0.196
  Angle     :  0.608   7.310  12938  Z= 0.309
  Chirality :  0.044   0.190   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.518  32.335   1252
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.06 (0.25), residues: 1166
  helix:  1.45 (0.30), residues: 300
  sheet: -0.36 (0.23), residues: 493
  loop : -0.62 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 243 
 HIS   0.005   0.001   HIS A 102 
 PHE   0.021   0.001   PHE A 120 
 TYR   0.028   0.002   TYR A 307 
 ARG   0.004   0.000   ARG I 140 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 326
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.9589 (mm) cc_final: 0.9189 (mt)
REVERT: A  152 LYS cc_start: 0.9330 (mttt) cc_final: 0.8679 (mmtp)
REVERT: A  169 GLN cc_start: 0.7642 (mt0) cc_final: 0.7248 (mt0)
REVERT: A  217 TYR cc_start: 0.7446 (t80) cc_final: 0.6764 (t80)
REVERT: A  219 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7368 (tpp80)
REVERT: A  259 LEU cc_start: 0.9251 (tp) cc_final: 0.8948 (tp)
REVERT: A  306 LYS cc_start: 0.8703 (tttp) cc_final: 0.8444 (tttm)
REVERT: A  314 TYR cc_start: 0.8716 (t80) cc_final: 0.8040 (t80)
REVERT: C   23 LYS cc_start: 0.8921 (mttt) cc_final: 0.8401 (mttp)
REVERT: D   50 GLN cc_start: 0.8191 (mm110) cc_final: 0.7800 (mm110)
REVERT: E   49 ASN cc_start: 0.8349 (p0) cc_final: 0.7917 (p0)
REVERT: G  397 LEU cc_start: 0.4102 (tp) cc_final: 0.3478 (pt)
REVERT: G  496 MET cc_start: -0.0284 (mpp) cc_final: -0.1261 (mtp)
REVERT: I  120 PHE cc_start: 0.8584 (t80) cc_final: 0.8215 (t80)
REVERT: I  132 ASP cc_start: 0.7954 (m-30) cc_final: 0.7670 (m-30)
REVERT: I  155 LEU cc_start: 0.8946 (mt) cc_final: 0.8718 (mt)
REVERT: I  178 VAL cc_start: 0.9224 (t) cc_final: 0.8982 (m)
REVERT: I  179 ASN cc_start: 0.8206 (t0) cc_final: 0.7784 (t0)
REVERT: I  227 ASP cc_start: 0.8383 (m-30) cc_final: 0.7899 (t0)
REVERT: I  310 ARG cc_start: 0.7768 (ptp90) cc_final: 0.7481 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8336 (p) cc_final: 0.7980 (p)
REVERT: I  359 PHE cc_start: 0.8436 (t80) cc_final: 0.7857 (t80)
REVERT: J   89 ARG cc_start: 0.5855 (tpt90) cc_final: 0.4157 (mtt90)
REVERT: J  113 LEU cc_start: 0.8849 (tp) cc_final: 0.8645 (tp)
REVERT: J  121 GLN cc_start: 0.7681 (mm110) cc_final: 0.7215 (mt0)
REVERT: K   22 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7738 (tp30)
REVERT: M   52 ASN cc_start: 0.8340 (m-40) cc_final: 0.8123 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 326
  average time/residue: 0.1847
  time to fit residues: 85.7719
Evaluate side-chains
  261 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 50 optimal weight:   20.0000
   chunk 112 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0970
   chunk 19 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0470
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
D  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.169569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.126517 restraints weight = 16564.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126294 restraints weight = 9856.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127779 restraints weight = 7686.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9537  Z= 0.165
  Angle     :  0.589   6.531  12938  Z= 0.300
  Chirality :  0.043   0.191   1450
  Planarity :  0.004   0.043   1667
  Dihedral  :  4.329  26.260   1252
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  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:  0.11 (0.25), residues: 1166
  helix:  1.67 (0.30), residues: 299
  sheet: -0.27 (0.23), residues: 495
  loop : -0.57 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 243 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.019   0.001   PHE I 201 
 TYR   0.022   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A  85 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 LYS cc_start: 0.9243 (mttt) cc_final: 0.8950 (mttp)
REVERT: A  156 GLN cc_start: 0.7839 (tp40) cc_final: 0.7485 (tp40)
REVERT: A  169 GLN cc_start: 0.7554 (mt0) cc_final: 0.7271 (mt0)
REVERT: A  217 TYR cc_start: 0.7384 (t80) cc_final: 0.6709 (t80)
REVERT: A  219 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7350 (tpp80)
REVERT: A  244 ILE cc_start: 0.9324 (pt) cc_final: 0.9010 (pt)
REVERT: A  259 LEU cc_start: 0.9213 (tp) cc_final: 0.8948 (tp)
REVERT: A  261 ARG cc_start: 0.8281 (tpt-90) cc_final: 0.7552 (tpt-90)
REVERT: C   23 LYS cc_start: 0.8846 (mttt) cc_final: 0.8592 (mttm)
REVERT: C   40 MET cc_start: 0.8354 (mpp) cc_final: 0.8131 (mpp)
REVERT: E   49 ASN cc_start: 0.8227 (p0) cc_final: 0.7793 (p0)
REVERT: G  397 LEU cc_start: 0.4085 (tp) cc_final: 0.3476 (pt)
REVERT: G  496 MET cc_start: -0.0242 (mpp) cc_final: -0.1298 (mtp)
REVERT: I  120 PHE cc_start: 0.8616 (t80) cc_final: 0.8367 (t80)
REVERT: I  132 ASP cc_start: 0.7878 (m-30) cc_final: 0.7637 (m-30)
REVERT: I  155 LEU cc_start: 0.8892 (mt) cc_final: 0.8671 (mt)
REVERT: I  159 ASP cc_start: 0.6599 (t70) cc_final: 0.6318 (t70)
REVERT: I  175 ASP cc_start: 0.6786 (p0) cc_final: 0.6551 (p0)
REVERT: I  178 VAL cc_start: 0.9147 (t) cc_final: 0.8930 (m)
REVERT: I  203 GLN cc_start: 0.7568 (tt0) cc_final: 0.6847 (tt0)
REVERT: I  310 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7422 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8276 (p) cc_final: 0.7960 (p)
REVERT: J  113 LEU cc_start: 0.8725 (tp) cc_final: 0.8497 (tp)
REVERT: J  121 GLN cc_start: 0.7685 (mm110) cc_final: 0.7183 (mt0)
REVERT: K   22 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7748 (tp30)
REVERT: M   52 ASN cc_start: 0.8336 (m-40) cc_final: 0.8074 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1944
  time to fit residues: 91.2519
Evaluate side-chains
  263 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0060
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** D  38 ASN ** 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 = 0.4099 r_free = 0.4099 target = 0.166898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.119858 restraints weight = 16586.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122730 restraints weight = 9242.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.124579 restraints weight = 6346.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9537  Z= 0.218
  Angle     :  0.613   7.012  12938  Z= 0.316
  Chirality :  0.044   0.180   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.384  25.254   1252
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.39 %
    Favored  : 98.51 %
  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:  0.16 (0.25), residues: 1166
  helix:  1.59 (0.29), residues: 304
  sheet: -0.20 (0.23), residues: 506
  loop : -0.50 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 243 
 HIS   0.005   0.001   HIS A 102 
 PHE   0.027   0.001   PHE E  35 
 TYR   0.025   0.002   TYR A 307 
 ARG   0.003   0.000   ARG I  72 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 311
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.8040 (m-80) cc_final: 0.7819 (m-10)
REVERT: A  152 LYS cc_start: 0.9202 (mttt) cc_final: 0.8743 (mttp)
REVERT: A  169 GLN cc_start: 0.7629 (mt0) cc_final: 0.7298 (mt0)
REVERT: A  217 TYR cc_start: 0.7448 (t80) cc_final: 0.6696 (t80)
REVERT: A  219 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7253 (tpp80)
REVERT: A  259 LEU cc_start: 0.9289 (tp) cc_final: 0.9015 (tp)
REVERT: D   50 GLN cc_start: 0.8273 (mm110) cc_final: 0.7811 (mm110)
REVERT: E   46 ASN cc_start: 0.8503 (p0) cc_final: 0.8295 (p0)
REVERT: E   49 ASN cc_start: 0.8184 (p0) cc_final: 0.7721 (p0)
REVERT: G  366 MET cc_start: 0.1966 (mmm) cc_final: 0.0048 (mtp)
REVERT: G  397 LEU cc_start: 0.4352 (tp) cc_final: 0.3147 (pt)
REVERT: G  422 ASN cc_start: 0.3489 (p0) cc_final: 0.3284 (p0)
REVERT: G  496 MET cc_start: -0.0564 (mpp) cc_final: -0.1524 (mtp)
REVERT: I   69 GLU cc_start: 0.8516 (mp0) cc_final: 0.8006 (mp0)
REVERT: I  120 PHE cc_start: 0.8642 (t80) cc_final: 0.8349 (t80)
REVERT: I  132 ASP cc_start: 0.8091 (m-30) cc_final: 0.7740 (m-30)
REVERT: I  150 ILE cc_start: 0.9254 (mp) cc_final: 0.9021 (mp)
REVERT: I  155 LEU cc_start: 0.8960 (mt) cc_final: 0.8754 (mt)
REVERT: I  310 ARG cc_start: 0.7817 (ptp90) cc_final: 0.7456 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8168 (t80) cc_final: 0.7895 (t80)
REVERT: J  113 LEU cc_start: 0.8839 (tp) cc_final: 0.8584 (tp)
REVERT: J  121 GLN cc_start: 0.7804 (mm110) cc_final: 0.7363 (mt0)
REVERT: J  125 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7014 (mt-10)
REVERT: K   22 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7676 (tp30)
REVERT: M   52 ASN cc_start: 0.8514 (m-40) cc_final: 0.8205 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 311
  average time/residue: 0.1896
  time to fit residues: 84.1616
Evaluate side-chains
  267 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0010
   chunk 38 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN
D  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.168700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.122332 restraints weight = 16639.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125193 restraints weight = 9401.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.126976 restraints weight = 6491.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9537  Z= 0.178
  Angle     :  0.616   7.710  12938  Z= 0.314
  Chirality :  0.043   0.177   1450
  Planarity :  0.004   0.042   1667
  Dihedral  :  4.282  24.243   1252
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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:  0.29 (0.26), residues: 1166
  helix:  1.76 (0.30), residues: 298
  sheet: -0.15 (0.24), residues: 491
  loop : -0.43 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP I 243 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.026   0.001   PHE E  35 
 TYR   0.019   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A  85 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.7721 (tp40) cc_final: 0.7336 (tp40)
REVERT: A  169 GLN cc_start: 0.7582 (mt0) cc_final: 0.7279 (mt0)
REVERT: A  217 TYR cc_start: 0.7471 (t80) cc_final: 0.7130 (t80)
REVERT: A  219 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7559 (tpp80)
REVERT: A  259 LEU cc_start: 0.9253 (tp) cc_final: 0.8957 (tp)
REVERT: A  279 MET cc_start: 0.6758 (mmm) cc_final: 0.5402 (ptp)
REVERT: A  355 CYS cc_start: 0.8254 (m) cc_final: 0.8032 (m)
REVERT: D   50 GLN cc_start: 0.8358 (mm110) cc_final: 0.8109 (mm-40)
REVERT: E   49 ASN cc_start: 0.8149 (p0) cc_final: 0.7695 (p0)
REVERT: G  397 LEU cc_start: 0.4349 (tp) cc_final: 0.3690 (pt)
REVERT: G  422 ASN cc_start: 0.3577 (p0) cc_final: 0.3337 (p0)
REVERT: G  496 MET cc_start: -0.0636 (mpp) cc_final: -0.1563 (mtp)
REVERT: I   69 GLU cc_start: 0.8417 (mp0) cc_final: 0.8019 (mp0)
REVERT: I  132 ASP cc_start: 0.8066 (m-30) cc_final: 0.7661 (m-30)
REVERT: I  155 LEU cc_start: 0.8930 (mt) cc_final: 0.8615 (mt)
REVERT: I  159 ASP cc_start: 0.6386 (t70) cc_final: 0.6131 (t70)
REVERT: I  175 ASP cc_start: 0.6898 (p0) cc_final: 0.6430 (p0)
REVERT: I  179 ASN cc_start: 0.8363 (t0) cc_final: 0.7709 (t0)
REVERT: I  310 ARG cc_start: 0.7820 (ptp90) cc_final: 0.7469 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8084 (t80) cc_final: 0.7802 (t80)
REVERT: J  113 LEU cc_start: 0.8861 (tp) cc_final: 0.8618 (tp)
REVERT: J  121 GLN cc_start: 0.7794 (mm110) cc_final: 0.7215 (mt0)
REVERT: K   22 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7731 (tp30)
REVERT: M   52 ASN cc_start: 0.8588 (m-40) cc_final: 0.8150 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2281
  time to fit residues: 102.1901
Evaluate side-chains
  274 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0980
   chunk 2 optimal weight:    0.5980
   chunk 69 optimal weight:    0.1980
   chunk 106 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 166 GLN
K  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.170442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127201 restraints weight = 16670.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.127303 restraints weight = 10343.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128754 restraints weight = 7746.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
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   0.043   9537  Z= 0.171
  Angle     :  0.621   8.030  12938  Z= 0.317
  Chirality :  0.044   0.285   1450
  Planarity :  0.004   0.040   1667
  Dihedral  :  4.216  23.278   1252
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  0.36 (0.26), residues: 1166
  helix:  1.78 (0.30), residues: 299
  sheet: -0.13 (0.24), residues: 493
  loop : -0.33 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 243 
 HIS   0.003   0.001   HIS A 102 
 PHE   0.022   0.001   PHE E  35 
 TYR   0.019   0.001   TYR A 307 
 ARG   0.007   0.000   ARG A 315 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7373 (ttt180)
REVERT: A  156 GLN cc_start: 0.7719 (tp40) cc_final: 0.7325 (tp40)
REVERT: A  169 GLN cc_start: 0.7542 (mt0) cc_final: 0.7282 (mt0)
REVERT: A  217 TYR cc_start: 0.7620 (t80) cc_final: 0.7267 (t80)
REVERT: A  219 ARG cc_start: 0.8302 (tpp80) cc_final: 0.7675 (tpp80)
REVERT: A  279 MET cc_start: 0.6929 (mmm) cc_final: 0.5569 (ptp)
REVERT: B  120 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7855 (mm-30)
REVERT: C   23 LYS cc_start: 0.8824 (mttt) cc_final: 0.8580 (mttp)
REVERT: D   54 MET cc_start: 0.8032 (tpt) cc_final: 0.7788 (tpp)
REVERT: E   46 ASN cc_start: 0.8465 (p0) cc_final: 0.8243 (p0)
REVERT: E   49 ASN cc_start: 0.8136 (p0) cc_final: 0.7729 (p0)
REVERT: G  397 LEU cc_start: 0.4249 (tp) cc_final: 0.3643 (pt)
REVERT: G  422 ASN cc_start: 0.3691 (p0) cc_final: 0.3425 (p0)
REVERT: G  496 MET cc_start: -0.0467 (mpp) cc_final: -0.1414 (mtp)
REVERT: I   69 GLU cc_start: 0.8363 (mp0) cc_final: 0.8025 (mp0)
REVERT: I   72 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6779 (mtm-85)
REVERT: I   94 MET cc_start: 0.6932 (tpt) cc_final: 0.6309 (tmm)
REVERT: I  145 TRP cc_start: 0.8314 (m100) cc_final: 0.6881 (m-10)
REVERT: I  155 LEU cc_start: 0.8856 (mt) cc_final: 0.8621 (mt)
REVERT: I  175 ASP cc_start: 0.6960 (p0) cc_final: 0.6644 (p0)
REVERT: I  203 GLN cc_start: 0.7751 (tt0) cc_final: 0.6965 (tt0)
REVERT: I  310 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7457 (ptm-80)
REVERT: I  359 PHE cc_start: 0.7964 (t80) cc_final: 0.7702 (t80)
REVERT: J  113 LEU cc_start: 0.8808 (tp) cc_final: 0.8550 (tp)
REVERT: J  121 GLN cc_start: 0.7672 (mm110) cc_final: 0.7062 (mt0)
REVERT: K   22 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7848 (tp30)
REVERT: M   52 ASN cc_start: 0.8486 (m-40) cc_final: 0.8133 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.1835
  time to fit residues: 80.9159
Evaluate side-chains
  275 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.166950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.125439 restraints weight = 16527.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124371 restraints weight = 10498.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125255 restraints weight = 7955.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9537  Z= 0.252
  Angle     :  0.662   8.694  12938  Z= 0.339
  Chirality :  0.045   0.179   1450
  Planarity :  0.004   0.043   1667
  Dihedral  :  4.471  23.271   1252
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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:  0.24 (0.26), residues: 1166
  helix:  1.59 (0.29), residues: 304
  sheet: -0.17 (0.24), residues: 503
  loop : -0.37 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP I 243 
 HIS   0.008   0.001   HIS G 355 
 PHE   0.023   0.002   PHE B 130 
 TYR   0.021   0.002   TYR A 307 
 ARG   0.007   0.001   ARG A 315 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLN cc_start: 0.7484 (mt0) cc_final: 0.7234 (mt0)
REVERT: A  219 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7168 (tpp80)
REVERT: A  279 MET cc_start: 0.6923 (mmm) cc_final: 0.6585 (mmm)
REVERT: A  294 GLN cc_start: 0.7887 (tp40) cc_final: 0.7452 (tp40)
REVERT: D   41 PHE cc_start: 0.8585 (m-80) cc_final: 0.8379 (m-10)
REVERT: D   56 MET cc_start: 0.7001 (ttm) cc_final: 0.6714 (ttm)
REVERT: E   46 ASN cc_start: 0.8553 (p0) cc_final: 0.8277 (p0)
REVERT: E   49 ASN cc_start: 0.8139 (p0) cc_final: 0.7708 (p0)
REVERT: G  366 MET cc_start: 0.1464 (mmm) cc_final: -0.0362 (mtp)
REVERT: G  397 LEU cc_start: 0.3655 (tp) cc_final: 0.2563 (pt)
REVERT: G  422 ASN cc_start: 0.3815 (p0) cc_final: 0.3534 (p0)
REVERT: G  496 MET cc_start: -0.0613 (mpp) cc_final: -0.1629 (mtp)
REVERT: I   72 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7163 (ttm110)
REVERT: I  159 ASP cc_start: 0.6476 (t70) cc_final: 0.6268 (t70)
REVERT: I  310 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7728 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8156 (t80) cc_final: 0.7898 (t80)
REVERT: J  113 LEU cc_start: 0.8800 (tp) cc_final: 0.8570 (tp)
REVERT: J  121 GLN cc_start: 0.7665 (mm110) cc_final: 0.7186 (mt0)
REVERT: J  125 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6965 (mt-10)
REVERT: K   22 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7851 (tp30)
REVERT: M   52 ASN cc_start: 0.8639 (m-40) cc_final: 0.8149 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1827
  time to fit residues: 79.4488
Evaluate side-chains
  266 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 111 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0170
   chunk 107 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  29 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 = 0.4133 r_free = 0.4133 target = 0.169391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.123200 restraints weight = 16667.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.126033 restraints weight = 9532.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127787 restraints weight = 6615.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9537  Z= 0.200
  Angle     :  0.668   8.119  12938  Z= 0.340
  Chirality :  0.045   0.178   1450
  Planarity :  0.004   0.039   1667
  Dihedral  :  4.343  23.179   1252
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  0.25 (0.26), residues: 1166
  helix:  1.60 (0.30), residues: 304
  sheet: -0.17 (0.24), residues: 503
  loop : -0.35 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 243 
 HIS   0.007   0.001   HIS M  29 
 PHE   0.023   0.001   PHE A 120 
 TYR   0.015   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A  85 

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.8406 (t0) cc_final: 0.8030 (t0)
REVERT: A  156 GLN cc_start: 0.7875 (tp40) cc_final: 0.7443 (tp40)
REVERT: A  169 GLN cc_start: 0.7547 (mt0) cc_final: 0.7278 (mt0)
REVERT: A  219 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7262 (tpp80)
REVERT: A  244 ILE cc_start: 0.9316 (pt) cc_final: 0.9010 (pt)
REVERT: A  279 MET cc_start: 0.6750 (mmm) cc_final: 0.6119 (mmm)
REVERT: A  294 GLN cc_start: 0.7454 (tp40) cc_final: 0.7166 (tp40)
REVERT: C   40 MET cc_start: 0.8338 (mpp) cc_final: 0.8118 (mpp)
REVERT: D   56 MET cc_start: 0.7011 (ttm) cc_final: 0.6737 (ttm)
REVERT: E   46 ASN cc_start: 0.8518 (p0) cc_final: 0.8230 (p0)
REVERT: E   49 ASN cc_start: 0.8041 (p0) cc_final: 0.7591 (p0)
REVERT: G  366 MET cc_start: 0.2106 (mmm) cc_final: -0.0039 (mtp)
REVERT: G  397 LEU cc_start: 0.3978 (tp) cc_final: 0.2799 (pt)
REVERT: G  422 ASN cc_start: 0.3775 (p0) cc_final: 0.3507 (p0)
REVERT: G  496 MET cc_start: -0.0809 (mpp) cc_final: -0.1753 (mtp)
REVERT: I   72 ARG cc_start: 0.7414 (ttm110) cc_final: 0.6949 (mtm-85)
REVERT: I  155 LEU cc_start: 0.8950 (mt) cc_final: 0.8741 (mt)
REVERT: I  310 ARG cc_start: 0.8260 (ptp90) cc_final: 0.7666 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8073 (t80) cc_final: 0.7835 (t80)
REVERT: J  113 LEU cc_start: 0.8847 (tp) cc_final: 0.8612 (tp)
REVERT: J  121 GLN cc_start: 0.7709 (mm110) cc_final: 0.7153 (mt0)
REVERT: K   22 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7820 (tp30)
REVERT: M   52 ASN cc_start: 0.8602 (m-40) cc_final: 0.8047 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.1826
  time to fit residues: 79.2774
Evaluate side-chains
  268 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 46 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0970
   chunk 89 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 ASN
D  38 ASN
K  17 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.169638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.127283 restraints weight = 16515.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126126 restraints weight = 10728.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.128220 restraints weight = 9019.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9537  Z= 0.201
  Angle     :  0.679  13.621  12938  Z= 0.344
  Chirality :  0.045   0.193   1450
  Planarity :  0.004   0.039   1667
  Dihedral  :  4.355  22.947   1252
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  0.25 (0.26), residues: 1166
  helix:  1.53 (0.30), residues: 304
  sheet: -0.13 (0.23), residues: 502
  loop : -0.36 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 243 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.022   0.001   PHE E  35 
 TYR   0.014   0.001   TYR A 307 
 ARG   0.003   0.000   ARG I 261 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3827.63 seconds
wall clock time: 68 minutes 8.04 seconds (4088.04 seconds total)