Starting phenix.real_space_refine
on Fri Jul 25 05:04:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hpe_52327/07_2025/9hpe_52327.cif"
  }
  resolution = 2.9
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    4515      2.51       5
     N    1222      2.21       5
     O    1312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7084
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 3067
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 375, 3045
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 375, 3045
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 3092
    Chain: "C"
      Number of atoms: 3959
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 491, 3948
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 473}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
      Conformer: "B"
        Number of residues, atoms: 491, 3948
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 473}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
          bond proxies already assigned to first conformer: 4022
    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
    Chain: "C"
      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
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG B 184 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG B 184 " occ=0.52
    residue:
      pdb=" N  AARG B 265 " occ=0.86
      ... (20 atoms not shown)
      pdb=" NH2BARG B 265 " occ=0.14
    residue:
      pdb=" N  AARG C 300 " occ=0.85
      ... (20 atoms not shown)
      pdb=" NH2BARG C 300 " occ=0.15
  Time building chain proxies: 10.53, per 1000 atoms: 1.49
  Number of scatterers: 7084
  At special positions: 0
  Unit cell: (84.252, 100.772, 113.988, 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      35     16.00
     O    1312      8.00
     N    1222      7.00
     C    4515      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  63 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  63 " - pdb=" SG  CYS C 312 " distance=2.03

  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
    NAG-ASN
      " NAG B1202 " - " ASN B 238 "
  Time building additional restraints: 2.66
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1634

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      41.9% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 32
    Processing helix  chain 'B' and resid 54 through 68
      removed outlier: 3.546A  pdb=" N   ARG B  68 " --> pdb=" O   SER B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 93
      removed outlier: 3.505A  pdb=" N   LEU B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 143 through 157
    Processing helix  chain 'B' and resid 170 through 184
      removed outlier: 3.886A  pdb=" N   PHE B 174 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 208
    Processing helix  chain 'B' and resid 229 through 234
      removed outlier: 3.860A  pdb=" N   HIS B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 260
    Processing helix  chain 'B' and resid 276 through 299
      removed outlier: 3.541A  pdb=" N   ALA B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 332
    Processing helix  chain 'C' and resid 16 through 32
    Processing helix  chain 'C' and resid 54 through 69
    Processing helix  chain 'C' and resid 81 through 92
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 143 through 157
    Processing helix  chain 'C' and resid 170 through 184
      removed outlier: 3.811A  pdb=" N   PHE C 174 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 209
    Processing helix  chain 'C' and resid 223 through 227
      removed outlier: 3.527A  pdb=" N   ILE C 227 " --> pdb=" O   PHE C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 235
    Processing helix  chain 'C' and resid 249 through 260
    Processing helix  chain 'C' and resid 276 through 299
    Processing helix  chain 'C' and resid 322 through 332
    Processing helix  chain 'C' and resid 425 through 439
    Processing helix  chain 'C' and resid 464 through 471
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 746 through 760
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 49
      removed outlier: 9.989A  pdb=" N   ALA B  72 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   SER B   7 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 8.689A  pdb=" N   PHE B  74 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   GLY B   9 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 164
      removed outlier: 6.987A  pdb=" N   PHE B 133 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ARG B 163 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TYR B 135 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   LYS B 132 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   LEU B 190 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ASP B 192 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU B 136 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR B 189 " --> pdb=" O   MET B 218 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   PHE B 242 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 337
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 49
      removed outlier: 10.305A  pdb=" N   ALA C  72 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   SER C   7 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   PHE C  74 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   GLY C   9 " --> pdb=" O   PHE C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 159 through 164
      removed outlier: 7.005A  pdb=" N   PHE C 133 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ARG C 163 " --> pdb=" O   PHE C 133 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   TYR C 135 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LYS C 132 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   LEU C 190 " --> pdb=" O   LYS C 132 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL C 134 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ASP C 192 " --> pdb=" O   VAL C 134 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU C 136 " --> pdb=" O   ASP C 192 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   TYR C 189 " --> pdb=" O   MET C 218 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   PHE C 242 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 335 through 337
    Processing sheet with id=AA7, first strand: chain 'C' and resid 396 through 401
    Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 410
    Processing sheet with id=AA9, first strand: chain 'C' and resid 454 through 455
      removed outlier: 3.688A  pdb=" N   ALA C 454 " --> pdb=" O   ASN C 463 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 491 through 493

    318 hydrogen bonds defined for protein.
    939 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: 2.27

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2322
        1.34 -     1.46: 1295
        1.46 -     1.57: 3564
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7242
  Sorted by residual:
  bond pdb=" C1  NAG B1202 "
       pdb=" O5  NAG B1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C1  NAG C1202 "
       pdb=" O5  NAG C1202 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C2  NAG C1202 "
       pdb=" N2  NAG C1202 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C1  NAG C1201 "
       pdb=" O5  NAG C1201 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.38e+00
  bond pdb=" C5  NAG C1201 "
       pdb=" O5  NAG C1201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 7237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 9360
        0.98 -     1.95: 342
        1.95 -     2.93: 82
        2.93 -     3.90: 19
        3.90 -     4.88: 6
  Bond angle restraints: 9809
  Sorted by residual:
  angle pdb=" N   VAL B 362 "
        pdb=" CA  VAL B 362 "
        pdb=" C   VAL B 362 "
      ideal   model   delta    sigma   weight residual
     110.21  107.46    2.75 1.13e+00 7.83e-01 5.94e+00
  angle pdb=" CA  GLU B 269 "
        pdb=" CB  GLU B 269 "
        pdb=" CG  GLU B 269 "
      ideal   model   delta    sigma   weight residual
     114.10  118.76   -4.66 2.00e+00 2.50e-01 5.43e+00
  angle pdb=" N   THR C  36 "
        pdb=" CA  THR C  36 "
        pdb=" CB  THR C  36 "
      ideal   model   delta    sigma   weight residual
     113.65  110.52    3.13 1.47e+00 4.63e-01 4.55e+00
  angle pdb=" C   ARG B  14 "
        pdb=" N   ASN B  15 "
        pdb=" CA  ASN B  15 "
      ideal   model   delta    sigma   weight residual
     122.46  125.30   -2.84 1.41e+00 5.03e-01 4.06e+00
  angle pdb=" C   GLU B 375 "
        pdb=" CA  GLU B 375 "
        pdb=" CB  GLU B 375 "
      ideal   model   delta    sigma   weight residual
     110.81  114.01   -3.20 1.65e+00 3.67e-01 3.76e+00
  ... (remaining 9804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 3933
       17.93 -    35.87: 335
       35.87 -    53.80: 52
       53.80 -    71.73: 20
       71.73 -    89.67: 5
  Dihedral angle restraints: 4345
    sinusoidal: 1803
      harmonic: 2542
  Sorted by residual:
  dihedral pdb=" CB  CYS C  63 "
           pdb=" SG  CYS C  63 "
           pdb=" SG  CYS C 312 "
           pdb=" CB  CYS C 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.57   69.57     1      1.00e+01 1.00e-02 6.25e+01
  dihedral pdb=" CB  CYS B  63 "
           pdb=" SG  CYS B  63 "
           pdb=" SG  CYS B 312 "
           pdb=" CB  CYS B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.31   54.31     1      1.00e+01 1.00e-02 4.00e+01
  dihedral pdb=" CA  GLU B 375 "
           pdb=" C   GLU B 375 "
           pdb=" N   ARG B 376 "
           pdb=" CA  ARG B 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 4342 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 695
       0.035 -    0.070: 285
       0.070 -    0.105: 66
       0.105 -    0.140: 29
       0.140 -    0.175: 1
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" C2  NAG C1202 "
            pdb=" C1  NAG C1202 "
            pdb=" C3  NAG C1202 "
            pdb=" N2  NAG C1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  VAL B 362 "
            pdb=" N   VAL B 362 "
            pdb=" C   VAL B 362 "
            pdb=" CB  VAL B 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE C 239 "
            pdb=" N   ILE C 239 "
            pdb=" C   ILE C 239 "
            pdb=" CB  ILE C 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1073 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 320 "    0.014 2.00e-02 2.50e+03   1.22e-02 3.75e+00
        pdb=" CG  TRP B 320 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 320 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 320 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 320 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 320 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 320 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 320 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 320 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B  99 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 748 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO C 749 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 749 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 749 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 172
        2.71 -     3.26: 6843
        3.26 -     3.81: 11353
        3.81 -     4.35: 14698
        4.35 -     4.90: 25267
  Nonbonded interactions: 58333
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 128 "
            pdb=" OE1 GLU C 359 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OE1 GLU C 404 "
            pdb=" OH  TYR C 452 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD2 ASP B 284 "
            pdb=" OG1 THR B 339 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD2 ASP C 182 "
            pdb=" OH  TYR C 215 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE2 GLU C  19 "
            pdb=" OG1 THR C 278 "
     model   vdw
     2.276 3.040
  ... (remaining 58328 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=0.14 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:             12.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     28.990
  Find NCS groups from input model:        0.090
  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:15.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
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   0.029   7245  Z= 0.126
  Angle     :  0.480   4.879   9816  Z= 0.267
  Chirality :  0.042   0.175   1076
  Planarity :  0.003   0.040   1266
  Dihedral  : 13.776  89.667   2705
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.00 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.57 (0.29), residues: 859
  helix:  1.92 (0.28), residues: 357
  sheet: -0.94 (0.41), residues: 141
  loop : -0.58 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 320 
 HIS   0.004   0.001   HIS B 211 
 PHE   0.009   0.001   PHE B 293 
 TYR   0.018   0.001   TYR C  45 
 ARG   0.002   0.000   ARG C 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       2.55620 (    3)
  hydrogen bonds       : bond        0.11261 (  318)
  hydrogen bonds       : angle       5.35801 (  939)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       1.05826 (    4)
  covalent geometry    : bond        0.00267 ( 7242)
  covalent geometry    : angle       0.47786 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: B  359 GLU cc_start: 0.7368 (tp30) cc_final: 0.7080 (mm-30)
REVERT: C  155 GLN cc_start: 0.7685 (tt0) cc_final: 0.7421 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 1.5682
  time to fit residues: 147.4545
Evaluate side-chains
  69 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 26 optimal weight:    0.1980
   chunk 40 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 352 ASN
C 185 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.085069 restraints weight = 49903.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.58
r_work: 0.2621 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7245  Z= 0.159
  Angle     :  0.512   9.614   9816  Z= 0.273
  Chirality :  0.044   0.244   1076
  Planarity :  0.004   0.039   1266
  Dihedral  :  5.093  54.334   1050
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  7.82 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.62 (0.29), residues: 859
  helix:  1.96 (0.27), residues: 361
  sheet: -0.96 (0.41), residues: 141
  loop : -0.57 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 320 
 HIS   0.007   0.001   HIS B 211 
 PHE   0.012   0.001   PHE B  23 
 TYR   0.019   0.001   TYR C 295 
 ARG   0.008   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00416 (    1)
  link_NAG-ASN         : angle       2.50964 (    3)
  hydrogen bonds       : bond        0.03935 (  318)
  hydrogen bonds       : angle       4.47997 (  939)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.98999 (    4)
  covalent geometry    : bond        0.00380 ( 7242)
  covalent geometry    : angle       0.51011 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8049 (t0) cc_final: 0.7800 (t0)
REVERT: B  359 GLU cc_start: 0.7544 (tp30) cc_final: 0.7296 (mm-30)
REVERT: C  155 GLN cc_start: 0.8045 (tt0) cc_final: 0.7762 (mt0)
  outliers start: 8
  outliers final: 4
  residues processed: 75
  average time/residue: 1.4035
  time to fit residues: 110.7346
Evaluate side-chains
  71 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  446 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.084884 restraints weight = 39153.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 4.10
r_work: 0.2699 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.129
  Angle     :  0.476   9.611   9816  Z= 0.256
  Chirality :  0.042   0.241   1076
  Planarity :  0.004   0.039   1266
  Dihedral  :  4.651  55.139   1050
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.15 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.70 (0.29), residues: 859
  helix:  2.09 (0.27), residues: 361
  sheet: -0.98 (0.41), residues: 141
  loop : -0.59 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 320 
 HIS   0.005   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B  23 
 TYR   0.016   0.001   TYR C 295 
 ARG   0.009   0.000   ARG C 265 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       2.50563 (    3)
  hydrogen bonds       : bond        0.03616 (  318)
  hydrogen bonds       : angle       4.28127 (  939)
  SS BOND              : bond        0.00030 (    2)
  SS BOND              : angle       0.84594 (    4)
  covalent geometry    : bond        0.00301 ( 7242)
  covalent geometry    : angle       0.47385 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8018 (t0) cc_final: 0.7770 (t0)
REVERT: B  359 GLU cc_start: 0.7472 (tp30) cc_final: 0.7238 (mm-30)
REVERT: C  155 GLN cc_start: 0.7965 (tt0) cc_final: 0.7756 (mt0)
REVERT: C  756 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7605 (mmtt)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 1.4658
  time to fit residues: 114.1415
Evaluate side-chains
  71 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 26 optimal weight:    0.0970
   chunk 13 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.084948 restraints weight = 44993.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 4.39
r_work: 0.2691 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.128
  Angle     :  0.472   9.636   9816  Z= 0.253
  Chirality :  0.042   0.244   1076
  Planarity :  0.004   0.039   1266
  Dihedral  :  4.470  55.154   1050
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.15 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.73 (0.29), residues: 859
  helix:  2.14 (0.27), residues: 361
  sheet: -0.99 (0.41), residues: 141
  loop : -0.59 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 320 
 HIS   0.005   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B  23 
 TYR   0.020   0.001   TYR C 295 
 ARG   0.009   0.000   ARG C 265 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    1)
  link_NAG-ASN         : angle       2.45981 (    3)
  hydrogen bonds       : bond        0.03550 (  318)
  hydrogen bonds       : angle       4.19853 (  939)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       0.80446 (    4)
  covalent geometry    : bond        0.00299 ( 7242)
  covalent geometry    : angle       0.46994 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8020 (t0) cc_final: 0.7764 (t0)
REVERT: B  359 GLU cc_start: 0.7504 (tp30) cc_final: 0.7268 (mm-30)
REVERT: C  756 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7636 (mmtt)
  outliers start: 11
  outliers final: 4
  residues processed: 77
  average time/residue: 1.4677
  time to fit residues: 118.4909
Evaluate side-chains
  74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0870
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 283 HIS
C 315 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.085147 restraints weight = 34633.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 3.95
r_work: 0.2706 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.121
  Angle     :  0.460   9.630   9816  Z= 0.247
  Chirality :  0.042   0.245   1076
  Planarity :  0.004   0.041   1266
  Dihedral  :  4.414  55.415   1050
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.68 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.81 (0.29), residues: 859
  helix:  2.21 (0.27), residues: 362
  sheet: -0.96 (0.42), residues: 141
  loop : -0.54 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 320 
 HIS   0.004   0.001   HIS B 211 
 PHE   0.010   0.001   PHE B  23 
 TYR   0.017   0.001   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       2.42426 (    3)
  hydrogen bonds       : bond        0.03455 (  318)
  hydrogen bonds       : angle       4.13881 (  939)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.73395 (    4)
  covalent geometry    : bond        0.00282 ( 7242)
  covalent geometry    : angle       0.45817 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8010 (t0) cc_final: 0.7732 (t0)
REVERT: B  359 GLU cc_start: 0.7511 (tp30) cc_final: 0.7273 (mm-30)
REVERT: C   38 GLU cc_start: 0.7973 (pm20) cc_final: 0.7711 (pm20)
REVERT: C  756 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7628 (mmtt)
  outliers start: 8
  outliers final: 5
  residues processed: 78
  average time/residue: 1.4924
  time to fit residues: 122.1332
Evaluate side-chains
  77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.083556 restraints weight = 38142.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 4.00
r_work: 0.2686 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7245  Z= 0.149
  Angle     :  0.485   9.656   9816  Z= 0.259
  Chirality :  0.043   0.251   1076
  Planarity :  0.004   0.041   1266
  Dihedral  :  4.491  55.250   1050
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.81 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.75 (0.29), residues: 859
  helix:  2.16 (0.27), residues: 362
  sheet: -1.01 (0.41), residues: 141
  loop : -0.57 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 320 
 HIS   0.006   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B 293 
 TYR   0.016   0.001   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    1)
  link_NAG-ASN         : angle       2.54616 (    3)
  hydrogen bonds       : bond        0.03692 (  318)
  hydrogen bonds       : angle       4.17550 (  939)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.71927 (    4)
  covalent geometry    : bond        0.00354 ( 7242)
  covalent geometry    : angle       0.48317 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8061 (t0) cc_final: 0.7770 (t0)
REVERT: B  359 GLU cc_start: 0.7539 (tp30) cc_final: 0.7286 (mm-30)
REVERT: C   38 GLU cc_start: 0.8001 (pm20) cc_final: 0.7751 (pm20)
REVERT: C  756 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7622 (mmtt)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 1.8995
  time to fit residues: 157.6728
Evaluate side-chains
  77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.109568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.083707 restraints weight = 36197.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.89
r_work: 0.2707 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7245  Z= 0.156
  Angle     :  0.499   9.655   9816  Z= 0.265
  Chirality :  0.043   0.252   1076
  Planarity :  0.004   0.043   1266
  Dihedral  :  4.551  55.274   1050
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.48 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.72 (0.29), residues: 859
  helix:  2.13 (0.27), residues: 362
  sheet: -1.04 (0.41), residues: 141
  loop : -0.57 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 320 
 HIS   0.006   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B 293 
 TYR   0.017   0.001   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    1)
  link_NAG-ASN         : angle       2.55955 (    3)
  hydrogen bonds       : bond        0.03726 (  318)
  hydrogen bonds       : angle       4.17700 (  939)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.72067 (    4)
  covalent geometry    : bond        0.00371 ( 7242)
  covalent geometry    : angle       0.49690 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8062 (t0) cc_final: 0.7773 (t0)
REVERT: B  359 GLU cc_start: 0.7379 (tp30) cc_final: 0.7103 (mm-30)
REVERT: C   38 GLU cc_start: 0.8018 (pm20) cc_final: 0.7806 (pm20)
REVERT: C  756 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7604 (mmtt)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 1.8588
  time to fit residues: 149.8212
Evaluate side-chains
  78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.083717 restraints weight = 41521.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 4.20
r_work: 0.2683 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7245  Z= 0.143
  Angle     :  0.501  12.384   9816  Z= 0.264
  Chirality :  0.043   0.252   1076
  Planarity :  0.004   0.042   1266
  Dihedral  :  4.523  55.359   1050
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.74 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.75 (0.29), residues: 859
  helix:  2.17 (0.27), residues: 362
  sheet: -1.03 (0.41), residues: 141
  loop : -0.56 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 320 
 HIS   0.006   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B 293 
 TYR   0.016   0.001   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    1)
  link_NAG-ASN         : angle       2.52690 (    3)
  hydrogen bonds       : bond        0.03621 (  318)
  hydrogen bonds       : angle       4.14416 (  939)
  SS BOND              : bond        0.00055 (    2)
  SS BOND              : angle       0.70651 (    4)
  covalent geometry    : bond        0.00339 ( 7242)
  covalent geometry    : angle       0.49884 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8032 (t0) cc_final: 0.7731 (t0)
REVERT: C   38 GLU cc_start: 0.8005 (pm20) cc_final: 0.7791 (pm20)
REVERT: C  756 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7625 (mmtt)
  outliers start: 9
  outliers final: 6
  residues processed: 78
  average time/residue: 1.9390
  time to fit residues: 159.2785
Evaluate side-chains
  77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.108900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.082745 restraints weight = 43444.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 4.26
r_work: 0.2645 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7245  Z= 0.170
  Angle     :  0.526  14.067   9816  Z= 0.276
  Chirality :  0.044   0.257   1076
  Planarity :  0.004   0.043   1266
  Dihedral  :  4.610  55.210   1050
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.88 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.67 (0.29), residues: 859
  helix:  2.09 (0.27), residues: 362
  sheet: -1.10 (0.41), residues: 140
  loop : -0.58 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 320 
 HIS   0.007   0.001   HIS B 211 
 PHE   0.012   0.002   PHE B 293 
 TYR   0.017   0.002   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    1)
  link_NAG-ASN         : angle       2.57734 (    3)
  hydrogen bonds       : bond        0.03851 (  318)
  hydrogen bonds       : angle       4.20869 (  939)
  SS BOND              : bond        0.00078 (    2)
  SS BOND              : angle       0.72249 (    4)
  covalent geometry    : bond        0.00407 ( 7242)
  covalent geometry    : angle       0.52416 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 1.613 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8066 (t0) cc_final: 0.7781 (t0)
REVERT: C  182 ASP cc_start: 0.8500 (t70) cc_final: 0.8296 (t0)
REVERT: C  756 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7647 (mmtt)
  outliers start: 7
  outliers final: 7
  residues processed: 76
  average time/residue: 1.7994
  time to fit residues: 145.9003
Evaluate side-chains
  76 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C 315 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.110182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.084074 restraints weight = 47498.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 4.47
r_work: 0.2695 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7245  Z= 0.135
  Angle     :  0.509  13.495   9816  Z= 0.267
  Chirality :  0.043   0.254   1076
  Planarity :  0.004   0.043   1266
  Dihedral  :  4.539  55.478   1050
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.14 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.75 (0.29), residues: 859
  helix:  2.18 (0.27), residues: 361
  sheet: -1.06 (0.41), residues: 140
  loop : -0.57 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 320 
 HIS   0.005   0.001   HIS B 211 
 PHE   0.011   0.001   PHE B 293 
 TYR   0.017   0.001   TYR C 432 
 ARG   0.009   0.000   ARG B 231 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00240 (    1)
  link_NAG-ASN         : angle       2.48744 (    3)
  hydrogen bonds       : bond        0.03574 (  318)
  hydrogen bonds       : angle       4.12926 (  939)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.70266 (    4)
  covalent geometry    : bond        0.00320 ( 7242)
  covalent geometry    : angle       0.50722 ( 9809)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: B  170 ASP cc_start: 0.8049 (t0) cc_final: 0.7775 (t0)
REVERT: C  756 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7702 (mmtt)
  outliers start: 7
  outliers final: 6
  residues processed: 76
  average time/residue: 1.3877
  time to fit residues: 110.9451
Evaluate side-chains
  74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain C residue   48 ASP
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 253 GLN
C  15 ASN
C 315 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.084739 restraints weight = 40659.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 4.13
r_work: 0.2699 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7245  Z= 0.121
  Angle     :  0.498  13.084   9816  Z= 0.262
  Chirality :  0.042   0.253   1076
  Planarity :  0.004   0.043   1266
  Dihedral  :  4.454  55.526   1050
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.80 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.82 (0.29), residues: 859
  helix:  2.27 (0.27), residues: 361
  sheet: -1.03 (0.41), residues: 140
  loop : -0.56 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 320 
 HIS   0.004   0.001   HIS B 211 
 PHE   0.010   0.001   PHE B  23 
 TYR   0.017   0.001   TYR C 432 
 ARG   0.011   0.000   ARG C 265 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    1)
  link_NAG-ASN         : angle       2.40563 (    3)
  hydrogen bonds       : bond        0.03424 (  318)
  hydrogen bonds       : angle       4.07714 (  939)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.67540 (    4)
  covalent geometry    : bond        0.00283 ( 7242)
  covalent geometry    : angle       0.49669 ( 9809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5937.97 seconds
wall clock time: 105 minutes 27.56 seconds (6327.56 seconds total)