Starting phenix.real_space_refine
on Mon Jun  9 21:40:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hq7_34946/06_2025/8hq7_34946.cif"
  }
  resolution = 2.7
  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=   0.039
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 3142 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      34      5.16       5
     C    5221      2.51       5
     N    1387      2.21       5
     O    1650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8292
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "M"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1665
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1642
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204}
    Chain: "H"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1756
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214}
    Chain: "L"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1658
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 7.72, per 1000 atoms: 0.93
  Number of scatterers: 8292
  At special positions: 0
  Unit cell: (136.96, 93.304, 124.12, 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      34     16.00
     O    1650      8.00
     N    1387      7.00
     C    5221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 149 " - pdb=" SG  CYS M 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 225 " - pdb=" SG  CYS N 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 136 " - pdb=" SG  CYS N 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 231 " - pdb=" SG  CYS L 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 24 sheets defined
      9.7% alpha, 44.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.709A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.957A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.428A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'M' and resid 28 through 32
    Processing helix  chain 'M' and resid 86 through 90
    Processing helix  chain 'M' and resid 165 through 167
      No H-bonds generated for 'chain 'M' and resid 165 through 167'
    Processing helix  chain 'M' and resid 194 through 199
      removed outlier: 4.071A  pdb=" N   GLY M 199 " --> pdb=" O   SER M 196 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 79 through 83
      removed outlier: 4.233A  pdb=" N   PHE N  83 " --> pdb=" O   PRO N  80 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 123 through 129
      removed outlier: 4.058A  pdb=" N   SER N 129 " --> pdb=" O   GLU N 125 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 185 through 190
      removed outlier: 3.988A  pdb=" N   LYS N 190 " --> pdb=" O   ALA N 186 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 67
      removed outlier: 3.560A  pdb=" N   ASN H  66 " --> pdb=" O   PRO H  63 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   ASN H  67 " --> pdb=" O   SER H  64 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 63 through 67'
    Processing helix  chain 'H' and resid 171 through 173
      No H-bonds generated for 'chain 'H' and resid 171 through 173'
    Processing helix  chain 'H' and resid 200 through 204
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.160A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.089A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 119 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   TYR M  33 " --> pdb=" O   GLU M  98 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   ARG M  38 " --> pdb=" O   TRP M  47 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   TRP M  47 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.089A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 119 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE M 111 " --> pdb=" O   ARG M  97 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   SER M  99 " --> pdb=" O   PHE M 109 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   PHE M 109 " --> pdb=" O   SER M  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 129 through 133
      removed outlier: 6.023A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'M' and resid 129 through 133
      removed outlier: 6.023A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 160 through 163
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.574A  pdb=" N   ASP N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.942A  pdb=" N   LEU N  33 " --> pdb=" O   SER N  49 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   SER N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13
      removed outlier: 4.014A  pdb=" N   SER N  99 " --> pdb=" O   GLN N  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 116 through 120
      removed outlier: 6.137A  pdb=" N   TYR N 175 " --> pdb=" O   ASN N 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 155 through 156
    Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.171A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.529A  pdb=" N   PHE H 101 " --> pdb=" O   PHE H 115 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   PHE H 115 " --> pdb=" O   PHE H 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.413A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.413A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER H 192 " --> pdb=" O   VAL H 184 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 166 through 169
      removed outlier: 3.849A  pdb=" N   TYR H 209 " --> pdb=" O   VAL H 226 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.989A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.915A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 146 through 151

    361 hydrogen bonds defined for protein.
    891 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: 2.64

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2658
        1.35 -     1.47: 2174
        1.47 -     1.59: 3621
        1.59 -     1.71: 0
        1.71 -     1.83: 40
  Bond restraints: 8493
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" CA  CYS A 379 "
       pdb=" CB  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.534  1.512  0.022 1.78e-02 3.16e+03 1.50e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.29e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" C3  NAG B   2 "
       pdb=" O3  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.01e+00
  ... (remaining 8488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.96: 11523
        3.96 -     7.91: 33
        7.91 -    11.87: 2
       11.87 -    15.82: 0
       15.82 -    19.78: 2
  Bond angle restraints: 11560
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  134.18  -19.78 2.30e+00 1.89e-01 7.40e+01
  angle pdb=" CA  CYS A 379 "
        pdb=" CB  CYS A 379 "
        pdb=" SG  CYS A 379 "
      ideal   model   delta    sigma   weight residual
     114.40  133.94  -19.54 2.30e+00 1.89e-01 7.22e+01
  angle pdb=" N   CYS A 379 "
        pdb=" CA  CYS A 379 "
        pdb=" C   CYS A 379 "
      ideal   model   delta    sigma   weight residual
     108.99  117.53   -8.54 1.57e+00 4.06e-01 2.96e+01
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     108.60  115.16   -6.56 1.46e+00 4.69e-01 2.02e+01
  angle pdb=" C   PRO H  14 "
        pdb=" N   THR H  15 "
        pdb=" CA  THR H  15 "
      ideal   model   delta    sigma   weight residual
     122.08  127.66   -5.58 1.47e+00 4.63e-01 1.44e+01
  ... (remaining 11555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4661
       16.21 -    32.42: 331
       32.42 -    48.62: 80
       48.62 -    64.83: 20
       64.83 -    81.04: 12
  Dihedral angle restraints: 5104
    sinusoidal: 1980
      harmonic: 3124
  Sorted by residual:
  dihedral pdb=" CA  ASP H 116 "
           pdb=" C   ASP H 116 "
           pdb=" N   PRO H 117 "
           pdb=" CA  PRO H 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -130.92  -49.08     0      5.00e+00 4.00e-02 9.64e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -4.96  -81.04     1      1.00e+01 1.00e-02 8.10e+01
  dihedral pdb=" CB  CYS M 149 "
           pdb=" SG  CYS M 149 "
           pdb=" SG  CYS M 205 "
           pdb=" CB  CYS M 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.58  -80.58     1      1.00e+01 1.00e-02 8.03e+01
  ... (remaining 5101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1181
       0.083 -    0.167: 114
       0.167 -    0.250: 1
       0.250 -    0.333: 1
       0.333 -    0.417: 1
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" CA  CYS A 379 "
            pdb=" N   CYS A 379 "
            pdb=" C   CYS A 379 "
            pdb=" CB  CYS A 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  THR H  15 "
            pdb=" N   THR H  15 "
            pdb=" C   THR H  15 "
            pdb=" CB  THR H  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.64e-01
  ... (remaining 1295 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H 116 "    0.057 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO H 117 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO H 117 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO H 117 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU M 157 "    0.051 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO M 158 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO M 158 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO M 158 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L  80 "    0.032 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO L  81 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 141
        2.68 -     3.24: 7354
        3.24 -     3.79: 12087
        3.79 -     4.35: 16965
        4.35 -     4.90: 28668
  Nonbonded interactions: 65215
  Sorted by model distance:
  nonbonded pdb=" OG  SER L 163 "
            pdb=" OG  SER L 177 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OD2 ASP N 172 "
            pdb=" OG1 THR N 174 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" CB  CYS A 379 "
            pdb=" CB  CYS A 432 "
     model   vdw
     2.212 3.072
  nonbonded pdb=" OD1 ASP M  61 "
            pdb=" NH2 ARG N  96 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG1 THR M 200 "
            pdb=" OE1 GLN M 201 "
     model   vdw
     2.301 3.040
  ... (remaining 65210 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.820
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.152
  Angle     :  0.738  19.780  11594  Z= 0.379
  Chirality :  0.047   0.417   1298
  Planarity :  0.006   0.086   1487
  Dihedral  : 12.536  77.415   3066
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.10 %

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:  0.23 (0.26), residues: 1072
  helix: -2.67 (0.55), residues: 57
  sheet:  1.41 (0.25), residues: 452
  loop : -0.61 (0.27), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 118 
 HIS   0.004   0.001   HIS N 191 
 PHE   0.011   0.001   PHE N 211 
 TYR   0.015   0.002   TYR H 160 
 ARG   0.004   0.000   ARG H  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.09992 (    3)
  link_BETA1-4         : bond        0.00232 (    1)
  link_BETA1-4         : angle       0.99809 (    3)
  hydrogen bonds       : bond        0.10947 (  317)
  hydrogen bonds       : angle       6.52206 (  891)
  SS BOND              : bond        0.00837 (   14)
  SS BOND              : angle       3.38717 (   28)
  covalent geometry    : bond        0.00342 ( 8493)
  covalent geometry    : angle       0.71975 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: M  208 ASN cc_start: 0.7153 (m110) cc_final: 0.6844 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 1.7403
  time to fit residues: 215.1903
Evaluate side-chains
  94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
M  13 GLN
M 208 ASN
N 162 GLN
L 125 GLN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.144461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105518 restraints weight = 13124.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.31
r_work: 0.3244 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.0877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8509  Z= 0.153
  Angle     :  0.671  14.768  11594  Z= 0.348
  Chirality :  0.046   0.225   1298
  Planarity :  0.006   0.083   1487
  Dihedral  :  5.526  55.441   1209
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  6.42 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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: 1072
  helix: -2.73 (0.52), residues: 58
  sheet:  1.47 (0.25), residues: 449
  loop : -0.63 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP N 150 
 HIS   0.007   0.001   HIS A 519 
 PHE   0.011   0.001   PHE N 211 
 TYR   0.015   0.002   TYR N 194 
 ARG   0.005   0.000   ARG A 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00027 (    1)
  link_NAG-ASN         : angle       1.16767 (    3)
  link_BETA1-4         : bond        0.00236 (    1)
  link_BETA1-4         : angle       1.11232 (    3)
  hydrogen bonds       : bond        0.03967 (  317)
  hydrogen bonds       : angle       5.65644 (  891)
  SS BOND              : bond        0.00687 (   14)
  SS BOND              : angle       2.64568 (   28)
  covalent geometry    : bond        0.00361 ( 8493)
  covalent geometry    : angle       0.65858 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8669 (mttp)
REVERT: M  208 ASN cc_start: 0.7267 (m-40) cc_final: 0.6985 (m110)
REVERT: H  105 ASP cc_start: 0.8247 (p0) cc_final: 0.7972 (p0)
REVERT: L   18 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7761 (ttm-80)
REVERT: L  166 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5563 (pp20)
  outliers start: 12
  outliers final: 2
  residues processed: 97
  average time/residue: 1.6076
  time to fit residues: 164.0017
Evaluate side-chains
  90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain L residue  166 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0970
   chunk 83 optimal weight:    0.0060
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
N 162 GLN
N 191 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.145479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.106418 restraints weight = 13345.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.33
r_work: 0.3259 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.119
  Angle     :  0.622  14.582  11594  Z= 0.322
  Chirality :  0.044   0.225   1298
  Planarity :  0.005   0.078   1487
  Dihedral  :  5.180  51.269   1209
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.05 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.33 (0.26), residues: 1072
  helix: -2.80 (0.53), residues: 57
  sheet:  1.44 (0.25), residues: 464
  loop : -0.53 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 118 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.009   0.001   PHE N 211 
 TYR   0.012   0.001   TYR H 160 
 ARG   0.004   0.000   ARG A 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       1.10248 (    3)
  link_BETA1-4         : bond        0.00225 (    1)
  link_BETA1-4         : angle       1.14441 (    3)
  hydrogen bonds       : bond        0.03554 (  317)
  hydrogen bonds       : angle       5.45503 (  891)
  SS BOND              : bond        0.00561 (   14)
  SS BOND              : angle       2.48498 (   28)
  covalent geometry    : bond        0.00272 ( 8493)
  covalent geometry    : angle       0.61013 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8675 (mttp)
REVERT: M  208 ASN cc_start: 0.7206 (m-40) cc_final: 0.7000 (m110)
REVERT: M  215 LYS cc_start: 0.5448 (mmtm) cc_final: 0.4703 (tptt)
REVERT: N  191 HIS cc_start: 0.4080 (m-70) cc_final: 0.3857 (m-70)
REVERT: H  105 ASP cc_start: 0.8003 (p0) cc_final: 0.7569 (p0)
REVERT: L   18 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7582 (ttm-80)
  outliers start: 14
  outliers final: 5
  residues processed: 96
  average time/residue: 1.6270
  time to fit residues: 163.9078
Evaluate side-chains
  87 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue  108 ILE
Chi-restraints excluded: chain N residue  109 LYS
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 61 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
H 212 ASN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.145002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105512 restraints weight = 13331.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.28
r_work: 0.3268 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.127
  Angle     :  0.622  11.970  11594  Z= 0.323
  Chirality :  0.045   0.198   1298
  Planarity :  0.005   0.077   1487
  Dihedral  :  5.039  47.222   1209
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.70 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.32 (0.26), residues: 1072
  helix: -2.77 (0.54), residues: 57
  sheet:  1.54 (0.25), residues: 450
  loop : -0.58 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 118 
 HIS   0.008   0.001   HIS A 519 
 PHE   0.009   0.001   PHE N 211 
 TYR   0.013   0.001   TYR H  96 
 ARG   0.005   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       1.10287 (    3)
  link_BETA1-4         : bond        0.00220 (    1)
  link_BETA1-4         : angle       1.22157 (    3)
  hydrogen bonds       : bond        0.03614 (  317)
  hydrogen bonds       : angle       5.36662 (  891)
  SS BOND              : bond        0.00576 (   14)
  SS BOND              : angle       2.38372 (   28)
  covalent geometry    : bond        0.00296 ( 8493)
  covalent geometry    : angle       0.61092 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8653 (mttp)
REVERT: M  215 LYS cc_start: 0.5396 (mmtm) cc_final: 0.4663 (tptt)
REVERT: N  191 HIS cc_start: 0.4155 (m-70) cc_final: 0.3916 (m-70)
REVERT: H  105 ASP cc_start: 0.8004 (p0) cc_final: 0.7587 (p0)
REVERT: L   18 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7594 (ttm-80)
REVERT: L  166 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5188 (pp20)
REVERT: L  195 CYS cc_start: 0.4722 (OUTLIER) cc_final: 0.4330 (t)
  outliers start: 19
  outliers final: 4
  residues processed: 98
  average time/residue: 1.5298
  time to fit residues: 158.0358
Evaluate side-chains
  89 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.145461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107637 restraints weight = 13243.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.44
r_work: 0.3267 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.116
  Angle     :  0.613  15.466  11594  Z= 0.317
  Chirality :  0.044   0.240   1298
  Planarity :  0.005   0.075   1487
  Dihedral  :  4.813  46.219   1209
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.87 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.37 (0.26), residues: 1072
  helix: -2.70 (0.55), residues: 57
  sheet:  1.71 (0.26), residues: 428
  loop : -0.60 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 118 
 HIS   0.008   0.001   HIS A 519 
 PHE   0.008   0.001   PHE N 211 
 TYR   0.011   0.001   TYR H  96 
 ARG   0.004   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00094 (    1)
  link_NAG-ASN         : angle       1.01848 (    3)
  link_BETA1-4         : bond        0.00251 (    1)
  link_BETA1-4         : angle       1.31674 (    3)
  hydrogen bonds       : bond        0.03421 (  317)
  hydrogen bonds       : angle       5.27920 (  891)
  SS BOND              : bond        0.00583 (   14)
  SS BOND              : angle       2.40386 (   28)
  covalent geometry    : bond        0.00269 ( 8493)
  covalent geometry    : angle       0.60147 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: M    3 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7925 (tt0)
REVERT: M   75 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8678 (mttp)
REVERT: M  215 LYS cc_start: 0.5276 (mmtm) cc_final: 0.4654 (tptt)
REVERT: N   79 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7202 (mp10)
REVERT: N  191 HIS cc_start: 0.4119 (m-70) cc_final: 0.3899 (m-70)
REVERT: L   18 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7481 (ttm-80)
REVERT: L  166 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5245 (pp20)
REVERT: L  195 CYS cc_start: 0.4580 (OUTLIER) cc_final: 0.4186 (t)
  outliers start: 23
  outliers final: 4
  residues processed: 95
  average time/residue: 1.5790
  time to fit residues: 158.3001
Evaluate side-chains
  89 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    3 GLN
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   79 GLN
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    0.0020
   chunk 93 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.144531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.105135 restraints weight = 13207.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.31
r_work: 0.3264 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8509  Z= 0.132
  Angle     :  0.630  13.942  11594  Z= 0.325
  Chirality :  0.045   0.241   1298
  Planarity :  0.005   0.076   1487
  Dihedral  :  4.753  47.020   1209
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.94 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.34 (0.26), residues: 1072
  helix: -2.75 (0.55), residues: 57
  sheet:  1.59 (0.25), residues: 449
  loop : -0.61 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP N 150 
 HIS   0.009   0.001   HIS A 519 
 PHE   0.010   0.001   PHE N 211 
 TYR   0.013   0.001   TYR H  96 
 ARG   0.005   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    1)
  link_NAG-ASN         : angle       1.06209 (    3)
  link_BETA1-4         : bond        0.00269 (    1)
  link_BETA1-4         : angle       1.41550 (    3)
  hydrogen bonds       : bond        0.03619 (  317)
  hydrogen bonds       : angle       5.31768 (  891)
  SS BOND              : bond        0.00650 (   14)
  SS BOND              : angle       2.45778 (   28)
  covalent geometry    : bond        0.00309 ( 8493)
  covalent geometry    : angle       0.61829 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8341 (m) cc_final: 0.8101 (p)
REVERT: M    3 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7931 (tt0)
REVERT: M   75 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8676 (mttp)
REVERT: M  215 LYS cc_start: 0.5327 (mmtm) cc_final: 0.4715 (tptt)
REVERT: N  191 HIS cc_start: 0.4305 (m-70) cc_final: 0.4054 (m-70)
REVERT: H  105 ASP cc_start: 0.7990 (p0) cc_final: 0.7597 (p0)
REVERT: L   78 ARG cc_start: 0.7025 (mmm160) cc_final: 0.6174 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5293 (pp20)
REVERT: L  195 CYS cc_start: 0.4748 (OUTLIER) cc_final: 0.4494 (t)
  outliers start: 18
  outliers final: 5
  residues processed: 94
  average time/residue: 1.5552
  time to fit residues: 154.0165
Evaluate side-chains
  91 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    3 GLN
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0170
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.144420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.105343 restraints weight = 13213.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.32
r_work: 0.3249 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8509  Z= 0.139
  Angle     :  0.648  16.573  11594  Z= 0.335
  Chirality :  0.045   0.258   1298
  Planarity :  0.005   0.076   1487
  Dihedral  :  4.776  47.173   1209
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.83 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.32 (0.26), residues: 1072
  helix: -2.76 (0.55), residues: 57
  sheet:  1.58 (0.25), residues: 449
  loop : -0.63 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP N 150 
 HIS   0.009   0.001   HIS A 519 
 PHE   0.010   0.001   PHE N 211 
 TYR   0.013   0.001   TYR H  96 
 ARG   0.005   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.06791 (    3)
  link_BETA1-4         : bond        0.00270 (    1)
  link_BETA1-4         : angle       1.41326 (    3)
  hydrogen bonds       : bond        0.03634 (  317)
  hydrogen bonds       : angle       5.34172 (  891)
  SS BOND              : bond        0.00707 (   14)
  SS BOND              : angle       2.57451 (   28)
  covalent geometry    : bond        0.00327 ( 8493)
  covalent geometry    : angle       0.63619 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8361 (m) cc_final: 0.8112 (p)
REVERT: M   75 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8669 (mttp)
REVERT: M  215 LYS cc_start: 0.5316 (mmtm) cc_final: 0.4694 (tptt)
REVERT: N  191 HIS cc_start: 0.4376 (m-70) cc_final: 0.4112 (m-70)
REVERT: H  105 ASP cc_start: 0.8058 (p0) cc_final: 0.7658 (p0)
REVERT: L   78 ARG cc_start: 0.7070 (mmm160) cc_final: 0.6053 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5339 (pp20)
REVERT: L  195 CYS cc_start: 0.4853 (OUTLIER) cc_final: 0.4562 (t)
  outliers start: 23
  outliers final: 9
  residues processed: 98
  average time/residue: 1.4902
  time to fit residues: 154.5888
Evaluate side-chains
  93 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0030
   chunk 14 optimal weight:    0.0970
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.144271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.105235 restraints weight = 13407.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.33
r_work: 0.3256 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8509  Z= 0.138
  Angle     :  0.649  15.855  11594  Z= 0.335
  Chirality :  0.046   0.267   1298
  Planarity :  0.005   0.076   1487
  Dihedral  :  4.775  47.193   1209
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.69 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.30 (0.26), residues: 1072
  helix: -2.80 (0.55), residues: 57
  sheet:  1.58 (0.25), residues: 455
  loop : -0.68 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP N 150 
 HIS   0.009   0.001   HIS A 519 
 PHE   0.010   0.001   PHE N 211 
 TYR   0.013   0.001   TYR H  96 
 ARG   0.004   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    1)
  link_NAG-ASN         : angle       1.08878 (    3)
  link_BETA1-4         : bond        0.00223 (    1)
  link_BETA1-4         : angle       1.37925 (    3)
  hydrogen bonds       : bond        0.03644 (  317)
  hydrogen bonds       : angle       5.31767 (  891)
  SS BOND              : bond        0.00728 (   14)
  SS BOND              : angle       2.74108 (   28)
  covalent geometry    : bond        0.00325 ( 8493)
  covalent geometry    : angle       0.63487 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8368 (m) cc_final: 0.8122 (p)
REVERT: M   75 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8680 (mttp)
REVERT: M  215 LYS cc_start: 0.5340 (mmtm) cc_final: 0.4707 (tptt)
REVERT: N  169 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7765 (m-30)
REVERT: N  191 HIS cc_start: 0.4331 (m-70) cc_final: 0.4057 (m-70)
REVERT: H  105 ASP cc_start: 0.8073 (p0) cc_final: 0.7687 (p0)
REVERT: L   78 ARG cc_start: 0.7073 (mmm160) cc_final: 0.6048 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5315 (pp20)
REVERT: L  195 CYS cc_start: 0.4929 (OUTLIER) cc_final: 0.4688 (t)
  outliers start: 19
  outliers final: 9
  residues processed: 93
  average time/residue: 1.5538
  time to fit residues: 152.3335
Evaluate side-chains
  94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  169 ASP
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 91 optimal weight:    0.1980
   chunk 43 optimal weight:    0.0870
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.144948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.105623 restraints weight = 13452.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.33
r_work: 0.3269 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8509  Z= 0.123
  Angle     :  0.637  14.962  11594  Z= 0.329
  Chirality :  0.045   0.242   1298
  Planarity :  0.005   0.075   1487
  Dihedral  :  4.651  45.983   1209
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.01 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.32 (0.26), residues: 1072
  helix: -2.82 (0.55), residues: 57
  sheet:  1.56 (0.25), residues: 451
  loop : -0.62 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 
 PHE   0.009   0.001   PHE N 211 
 TYR   0.011   0.001   TYR H  96 
 ARG   0.004   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00095 (    1)
  link_NAG-ASN         : angle       1.05951 (    3)
  link_BETA1-4         : bond        0.00270 (    1)
  link_BETA1-4         : angle       1.31533 (    3)
  hydrogen bonds       : bond        0.03427 (  317)
  hydrogen bonds       : angle       5.24687 (  891)
  SS BOND              : bond        0.00629 (   14)
  SS BOND              : angle       2.57569 (   28)
  covalent geometry    : bond        0.00289 ( 8493)
  covalent geometry    : angle       0.62456 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8361 (m) cc_final: 0.8117 (p)
REVERT: M   75 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8670 (mttp)
REVERT: M  215 LYS cc_start: 0.5360 (mmtm) cc_final: 0.4768 (tptt)
REVERT: N  191 HIS cc_start: 0.4214 (m-70) cc_final: 0.3993 (m-70)
REVERT: L   78 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6195 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5344 (pp20)
REVERT: L  195 CYS cc_start: 0.4865 (OUTLIER) cc_final: 0.4603 (t)
  outliers start: 19
  outliers final: 9
  residues processed: 95
  average time/residue: 1.4881
  time to fit residues: 149.2515
Evaluate side-chains
  91 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0010
   chunk 60 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0870
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4964

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.145376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.106461 restraints weight = 13239.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.30
r_work: 0.3280 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.116
  Angle     :  0.638  14.935  11594  Z= 0.330
  Chirality :  0.045   0.264   1298
  Planarity :  0.005   0.074   1487
  Dihedral  :  4.628  45.031   1209
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.22 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.35 (0.26), residues: 1072
  helix: -3.05 (0.56), residues: 51
  sheet:  1.71 (0.26), residues: 431
  loop : -0.63 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 
 PHE   0.008   0.001   PHE N 211 
 TYR   0.011   0.001   TYR H  96 
 ARG   0.007   0.000   ARG N  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00112 (    1)
  link_NAG-ASN         : angle       1.03629 (    3)
  link_BETA1-4         : bond        0.00328 (    1)
  link_BETA1-4         : angle       1.25241 (    3)
  hydrogen bonds       : bond        0.03334 (  317)
  hydrogen bonds       : angle       5.18442 (  891)
  SS BOND              : bond        0.00671 (   14)
  SS BOND              : angle       2.75071 (   28)
  covalent geometry    : bond        0.00269 ( 8493)
  covalent geometry    : angle       0.62413 (11560)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8359 (m) cc_final: 0.8106 (p)
REVERT: M   75 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (mttp)
REVERT: M  215 LYS cc_start: 0.5312 (mmtm) cc_final: 0.4762 (tptt)
REVERT: N  191 HIS cc_start: 0.4182 (m-70) cc_final: 0.3970 (m-70)
REVERT: L   78 ARG cc_start: 0.7192 (mmm160) cc_final: 0.6178 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5495 (pp20)
REVERT: L  195 CYS cc_start: 0.4692 (OUTLIER) cc_final: 0.4351 (t)
  outliers start: 15
  outliers final: 8
  residues processed: 89
  average time/residue: 1.6103
  time to fit residues: 150.7922
Evaluate side-chains
  88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  134 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 103 optimal weight:    0.2980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.144207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.104865 restraints weight = 13334.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.39
r_work: 0.3260 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8509  Z= 0.146
  Angle     :  0.676  17.529  11594  Z= 0.349
  Chirality :  0.046   0.278   1298
  Planarity :  0.005   0.076   1487
  Dihedral  :  4.798  46.413   1209
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.22 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    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:  0.27 (0.26), residues: 1072
  helix: -3.12 (0.55), residues: 51
  sheet:  1.58 (0.25), residues: 452
  loop : -0.71 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP N 150 
 HIS   0.010   0.001   HIS A 519 
 PHE   0.011   0.001   PHE L 119 
 TYR   0.014   0.002   TYR H  96 
 ARG   0.003   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00063 (    1)
  link_NAG-ASN         : angle       1.11550 (    3)
  link_BETA1-4         : bond        0.00148 (    1)
  link_BETA1-4         : angle       1.22538 (    3)
  hydrogen bonds       : bond        0.03643 (  317)
  hydrogen bonds       : angle       5.28370 (  891)
  SS BOND              : bond        0.00800 (   14)
  SS BOND              : angle       2.97076 (   28)
  covalent geometry    : bond        0.00345 ( 8493)
  covalent geometry    : angle       0.66091 (11560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8369.87 seconds
wall clock time: 143 minutes 19.97 seconds (8599.97 seconds total)