Starting phenix.real_space_refine
on Thu Jul  2 03:53:50 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2026/8e4c_27888.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.041
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      25      5.16       5
     C    4094      2.51       5
     N    1070      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6398
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1988
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 18, 'TRANS': 234}
    Chain: "A"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1988
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 18, 'TRANS': 234}
    Chain: "C"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1130
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 12, 'TRANS': 129}
    Chain: "D"
      Number of atoms: 1222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1222
          Classifications: {'peptide': 157}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 22
    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 chiralities: 2
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.00, per 1000 atoms: 0.16
  Number of scatterers: 6398
  At special positions: 0
  Unit cell: (73.04, 107.9, 156.04, 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      25     16.00
     O    1209      8.00
     N    1070      7.00
     C    4094      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 246 " - pdb=" SG  CYS B 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 353 " - pdb=" SG  CYS B 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 246 " - pdb=" SG  CYS A 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 353 " - pdb=" SG  CYS A 415 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 113 " - pdb=" SG  CYS D 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 124 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 120 " 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 C 401 " - " ASN C  58 "
      " NAG C 402 " - " ASN C  68 "
      " NAG D 301 " - " ASN D  68 "
      " NAG D 302 " - " ASN D  99 "
      " NAG D 303 " - " ASN D 130 "
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 233.1 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1518

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      27.5% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 3.919A  pdb=" N   ILE B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 299
      removed outlier: 3.651A  pdb=" N   TRP B 297 " --> pdb=" O   CYS B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 344
    Processing helix  chain 'B' and resid 404 through 409
    Processing helix  chain 'B' and resid 444 through 476
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 339 through 345
      removed outlier: 3.715A  pdb=" N   LEU A 345 " --> pdb=" O   GLU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.646A  pdb=" N   SER A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 476
      removed outlier: 4.176A  pdb=" N   TRP A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 96
      removed outlier: 3.631A  pdb=" N   ARG C  96 " --> pdb=" O   LYS C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 169
      Proline residue:  C 153  - end of helix
    Processing helix  chain 'D' and resid 111 through 115
    Processing helix  chain 'D' and resid 148 through 184
      removed outlier: 3.760A  pdb=" N   ARG D 152 " --> pdb=" O   ASP D 148 " (cutoff:3.500A)
      Proline residue:  D 175  - end of helix
      removed outlier: 3.639A  pdb=" N   ASP D 181 " --> pdb=" O   PHE D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 203
    Processing helix  chain 'D' and resid 208 through 213
    Processing sheet with id=AA1, first strand: chain 'B' and resid 225 through 229
      removed outlier: 3.532A  pdb=" N   THR B 245 " --> pdb=" O   ILE B 229 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   VAL B 292 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR B 245 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ALA B 290 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU B 247 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   GLY B 288 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   SER B 249 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 286 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 274 " --> pdb=" O   LYS B 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 263
      removed outlier: 3.647A  pdb=" N   ILE B 320 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   CYS B 305 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS B 318 " --> pdb=" O   CYS B 305 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 332 through 336
      removed outlier: 3.791A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 354 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 352 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 355 " --> pdb=" O   THR B 396 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   TYR B 394 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 336
      removed outlier: 3.791A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 354 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 352 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373
      removed outlier: 3.533A  pdb=" N   THR B 414 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS B 415 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG B 429 " --> pdb=" O   CYS B 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 228
      removed outlier: 5.807A  pdb=" N   PHE A 284 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 228
      removed outlier: 5.807A  pdb=" N   PHE A 284 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A 274 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 263
      removed outlier: 3.775A  pdb=" N   CYS A 305 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LYS A 318 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 307 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN A 316 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 336
      removed outlier: 3.508A  pdb=" N   SER A 398 " --> pdb=" O   CYS A 353 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 332 through 336
      removed outlier: 5.959A  pdb=" N   TYR A 394 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 372 through 373
      removed outlier: 3.745A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 75
      removed outlier: 3.545A  pdb=" N   TRP C 100 " --> pdb=" O   TRP C  62 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL C 103 " --> pdb=" O   LYS C 110 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS C 110 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 74 through 75
      removed outlier: 3.545A  pdb=" N   TRP C 100 " --> pdb=" O   TRP C  62 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY C  97 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 54 through 55
    Processing sheet with id=AB6, first strand: chain 'D' and resid 62 through 63

    281 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1415
        1.33 -     1.45: 1448
        1.45 -     1.57: 3663
        1.57 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 6557
  Sorted by residual:
  bond pdb=" CE1 HIS A 424 "
       pdb=" NE2 HIS A 424 "
    ideal  model  delta    sigma   weight residual
    1.321  1.363 -0.042 1.00e-02 1.00e+04 1.77e+01
  bond pdb=" CE1 HIS B 419 "
       pdb=" NE2 HIS B 419 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.71e+01
  bond pdb=" CE1 HIS C  95 "
       pdb=" NE2 HIS C  95 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.65e+01
  bond pdb=" CE1 HIS B 397 "
       pdb=" NE2 HIS B 397 "
    ideal  model  delta    sigma   weight residual
    1.321  1.360 -0.039 1.00e-02 1.00e+04 1.55e+01
  bond pdb=" N   ILE C  59 "
       pdb=" CA  ILE C  59 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.18e-02 7.18e+03 1.06e+01
  ... (remaining 6552 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 8800
        2.90 -     5.80: 121
        5.80 -     8.69: 8
        8.69 -    11.59: 3
       11.59 -    14.49: 1
  Bond angle restraints: 8933
  Sorted by residual:
  angle pdb=" N   GLU B 443 "
        pdb=" CA  GLU B 443 "
        pdb=" CB  GLU B 443 "
      ideal   model   delta    sigma   weight residual
     110.49  124.98  -14.49 1.69e+00 3.50e-01 7.35e+01
  angle pdb=" C   PRO C  57 "
        pdb=" CA  PRO C  57 "
        pdb=" CB  PRO C  57 "
      ideal   model   delta    sigma   weight residual
     111.56  101.97    9.59 1.65e+00 3.67e-01 3.38e+01
  angle pdb=" N   ASN D 130 "
        pdb=" CA  ASN D 130 "
        pdb=" C   ASN D 130 "
      ideal   model   delta    sigma   weight residual
     108.63  101.14    7.49 1.60e+00 3.91e-01 2.19e+01
  angle pdb=" CA  PRO D  42 "
        pdb=" N   PRO D  42 "
        pdb=" CD  PRO D  42 "
      ideal   model   delta    sigma   weight residual
     112.00  105.45    6.55 1.40e+00 5.10e-01 2.19e+01
  angle pdb=" C   ASN C  58 "
        pdb=" CA  ASN C  58 "
        pdb=" CB  ASN C  58 "
      ideal   model   delta    sigma   weight residual
     109.90  116.92   -7.02 1.56e+00 4.11e-01 2.03e+01
  ... (remaining 8928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3382
       17.92 -    35.85: 377
       35.85 -    53.77: 103
       53.77 -    71.70: 22
       71.70 -    89.62: 7
  Dihedral angle restraints: 3891
    sinusoidal: 1556
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" N   GLU B 443 "
           pdb=" C   GLU B 443 "
           pdb=" CA  GLU B 443 "
           pdb=" CB  GLU B 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.13  -35.33     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" C   GLU B 443 "
           pdb=" N   GLU B 443 "
           pdb=" CA  GLU B 443 "
           pdb=" CB  GLU B 443 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.37   32.77     0      2.50e+00 1.60e-01 1.72e+02
  dihedral pdb=" C   PRO C  57 "
           pdb=" N   PRO C  57 "
           pdb=" CA  PRO C  57 "
           pdb=" CB  PRO C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -108.74  -11.96     0      2.50e+00 1.60e-01 2.29e+01
  ... (remaining 3888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.291: 1034
       0.291 -    0.581: 2
       0.581 -    0.872: 0
       0.872 -    1.162: 0
       1.162 -    1.453: 1
  Chirality restraints: 1037
  Sorted by residual:
  chirality pdb=" CA  GLU B 443 "
            pdb=" N   GLU B 443 "
            pdb=" C   GLU B 443 "
            pdb=" CB  GLU B 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.06    1.45 2.00e-01 2.50e+01 5.27e+01
  chirality pdb=" C1  NAG C 401 "
            pdb=" ND2 ASN C  58 "
            pdb=" C2  NAG C 401 "
            pdb=" O5  NAG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CA  ILE C  69 "
            pdb=" N   ILE C  69 "
            pdb=" C   ILE C  69 "
            pdb=" CB  ILE C  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 1034 not shown)

  Planarity restraints: 1138
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 402 "   -0.277 2.00e-02 2.50e+03   2.37e-01 7.00e+02
        pdb=" C7  NAG C 402 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG C 402 "   -0.167 2.00e-02 2.50e+03
        pdb=" N2  NAG C 402 "    0.412 2.00e-02 2.50e+03
        pdb=" O7  NAG C 402 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 401 "    0.205 2.00e-02 2.50e+03   1.74e-01 3.80e+02
        pdb=" C7  NAG C 401 "   -0.040 2.00e-02 2.50e+03
        pdb=" C8  NAG C 401 "   -0.035 2.00e-02 2.50e+03
        pdb=" N2  NAG C 401 "   -0.287 2.00e-02 2.50e+03
        pdb=" O7  NAG C 401 "    0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 302 "   -0.170 2.00e-02 2.50e+03   1.45e-01 2.63e+02
        pdb=" C7  NAG D 302 "    0.032 2.00e-02 2.50e+03
        pdb=" C8  NAG D 302 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG D 302 "    0.238 2.00e-02 2.50e+03
        pdb=" O7  NAG D 302 "   -0.132 2.00e-02 2.50e+03
  ... (remaining 1135 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1222
        2.78 -     3.31: 6087
        3.31 -     3.84: 10132
        3.84 -     4.37: 11183
        4.37 -     4.90: 19265
  Nonbonded interactions: 47889
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 131 "
            pdb=" OG1 THR C 134 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR A 414 "
            pdb=" O   ARG A 429 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   SER A 382 "
            pdb=" OG1 THR A 396 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   VAL C 152 "
            pdb=" OG1 THR C 155 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   CYS D  43 "
            pdb=" OG1 THR D 132 "
     model   vdw
     2.357 3.040
  ... (remaining 47884 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.520
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.130
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4907
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      :  0.005   0.048   6570  Z= 0.339
  Angle     :  0.848  14.491   8964  Z= 0.515
  Chirality :  0.073   1.453   1037
  Planarity :  0.011   0.237   1133
  Dihedral  : 16.475  89.622   2349
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 22.46 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.31), residues: 793
  helix:  1.29 (0.38), residues: 196
  sheet: -0.42 (0.36), residues: 240
  loop : -0.69 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 118 
 TYR   0.014   0.001   TYR C 116 
 PHE   0.022   0.001   PHE D 119 
 TRP   0.042   0.001   TRP B 450 
 HIS   0.008   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.34 ( 6557)
  covalent geometry    : angle       0.83843 /  0.51 ( 8933)
  SS BOND              : bond        0.01155 /  0.37 (    8)
  SS BOND              : angle       1.47526 /  0.90 (   16)
  hydrogen bonds       : bond        0.20036 / 13.02 (  258)
  hydrogen bonds       : angle       9.50777 /  6.56 (  750)
  link_NAG-ASN         : bond        0.01638 /  0.86 (    5)
  link_NAG-ASN         : angle       3.00486 /  1.71 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  297 TRP cc_start: 0.2872 (t-100) cc_final: 0.0894 (t-100)
REVERT: B  351 VAL cc_start: 0.7019 (t) cc_final: 0.6666 (m)
REVERT: B  408 ASN cc_start: 0.6788 (m-40) cc_final: 0.6554 (m110)
REVERT: B  409 SER cc_start: 0.7094 (p) cc_final: 0.6880 (m)
REVERT: B  462 LEU cc_start: 0.6787 (mp) cc_final: 0.6301 (tp)
REVERT: C   55 ARG cc_start: 0.1671 (mtt180) cc_final: 0.1105 (mmt180)
REVERT: C   71 TRP cc_start: 0.4693 (m100) cc_final: 0.4420 (m100)
REVERT: C  162 ARG cc_start: 0.2063 (ttp-110) cc_final: 0.0962 (mmt180)
REVERT: D  103 TYR cc_start: 0.5257 (m-80) cc_final: 0.4896 (m-80)
REVERT: D  144 PHE cc_start: 0.6547 (p90) cc_final: 0.6092 (p90)
  outliers start: 13
  outliers final: 6
  residues processed: 163
  average time/residue: 0.0742
  time to fit residues: 15.4653
Evaluate side-chains
  96 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  160 ARG
Chi-restraints excluded: chain D residue  164 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 279 HIS
A 372 GLN
A 408 ASN
C  52 ASN
D  83 GLN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.189300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 111)---------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.183845 restraints weight = 18972.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 128)---------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.181165 restraints weight = 29119.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 90)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.180886 restraints weight = 34463.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.180829 restraints weight = 34748.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 69)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.180840 restraints weight = 32611.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4507
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6570  Z= 0.152
  Angle     :  0.716   9.609   8964  Z= 0.353
  Chirality :  0.048   0.270   1037
  Planarity :  0.006   0.075   1133
  Dihedral  :  6.217  63.425    861
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.61 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.30), residues: 793
  helix:  1.28 (0.36), residues: 198
  sheet: -0.55 (0.34), residues: 252
  loop : -0.71 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 340 
 TYR   0.020   0.002   TYR B 254 
 PHE   0.018   0.002   PHE D 119 
 TRP   0.019   0.001   TRP B 450 
 HIS   0.013   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 6557)
  covalent geometry    : angle       0.70249 /  0.35 ( 8933)
  SS BOND              : bond        0.00532 /  0.26 (    8)
  SS BOND              : angle       0.93426 /  0.49 (   16)
  hydrogen bonds       : bond        0.04417 /  2.95 (  258)
  hydrogen bonds       : angle       6.67667 /  4.59 (  750)
  link_NAG-ASN         : bond        0.00710 /  0.41 (    5)
  link_NAG-ASN         : angle       3.39890 /  2.13 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  351 VAL cc_start: 0.6798 (t) cc_final: 0.6584 (m)
REVERT: B  381 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7539 (m)
REVERT: B  402 VAL cc_start: 0.7195 (m) cc_final: 0.6985 (m)
REVERT: B  409 SER cc_start: 0.6242 (p) cc_final: 0.5830 (m)
REVERT: C   55 ARG cc_start: 0.2020 (mtt180) cc_final: 0.1303 (mmt180)
REVERT: C   71 TRP cc_start: 0.4689 (m100) cc_final: 0.4438 (m100)
REVERT: C  147 LEU cc_start: 0.7055 (tp) cc_final: 0.6645 (tp)
REVERT: C  162 ARG cc_start: 0.1743 (ttp-110) cc_final: 0.1008 (mmt180)
REVERT: D  144 PHE cc_start: 0.5705 (p90) cc_final: 0.5373 (p90)
  outliers start: 30
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0685
  time to fit residues: 10.5166
Evaluate side-chains
  105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  148 PHE
Chi-restraints excluded: chain D residue  164 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0370
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0070
   overall best weight:    0.5076

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
D 108 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.190668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.185018 restraints weight = 19312.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.184452 restraints weight = 30360.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.184612 restraints weight = 26404.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.184466 restraints weight = 25675.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.184501 restraints weight = 22572.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4356
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6570  Z= 0.139
  Angle     :  0.701  17.782   8964  Z= 0.339
  Chirality :  0.046   0.222   1037
  Planarity :  0.005   0.061   1133
  Dihedral  :  5.496  53.353    856
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 21.05 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.30), residues: 793
  helix:  1.40 (0.36), residues: 198
  sheet: -0.56 (0.33), residues: 250
  loop : -0.61 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.022   0.001   TYR B 254 
 PHE   0.025   0.002   PHE A 456 
 TRP   0.017   0.001   TRP C 100 
 HIS   0.008   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 6557)
  covalent geometry    : angle       0.65700 /  0.33 ( 8933)
  SS BOND              : bond        0.00459 /  0.25 (    8)
  SS BOND              : angle       0.93856 /  0.49 (   16)
  hydrogen bonds       : bond        0.03908 /  2.62 (  258)
  hydrogen bonds       : angle       5.98033 /  4.17 (  750)
  link_NAG-ASN         : bond        0.02269 /  1.70 (    5)
  link_NAG-ASN         : angle       5.97699 /  3.31 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 92
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  351 VAL cc_start: 0.6866 (t) cc_final: 0.6649 (m)
REVERT: B  364 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.6149 (t)
REVERT: C   55 ARG cc_start: 0.1914 (mtt180) cc_final: 0.1227 (mmt180)
REVERT: C  147 LEU cc_start: 0.6918 (tp) cc_final: 0.6593 (tp)
REVERT: C  162 ARG cc_start: 0.1639 (ttp-110) cc_final: 0.0973 (mmt180)
REVERT: D  144 PHE cc_start: 0.5709 (p90) cc_final: 0.5422 (p90)
  outliers start: 42
  outliers final: 24
  residues processed: 119
  average time/residue: 0.0658
  time to fit residues: 10.2132
Evaluate side-chains
  104 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  148 PHE
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  108 GLN
Chi-restraints excluded: chain D residue  174 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 19 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0370
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
D 129 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.191539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.186293 restraints weight = 19279.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.184869 restraints weight = 28063.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.184887 restraints weight = 29257.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.184452 restraints weight = 27499.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.184497 restraints weight = 24911.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4397
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6570  Z= 0.134
  Angle     :  0.720  15.622   8964  Z= 0.338
  Chirality :  0.045   0.208   1037
  Planarity :  0.005   0.059   1133
  Dihedral  :  5.068  47.355    853
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.60 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.30), residues: 793
  helix:  1.39 (0.36), residues: 199
  sheet: -0.55 (0.33), residues: 251
  loop : -0.47 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  79 
 TYR   0.022   0.001   TYR B 254 
 PHE   0.018   0.001   PHE D 119 
 TRP   0.019   0.001   TRP B 297 
 HIS   0.008   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 6557)
  covalent geometry    : angle       0.65208 /  0.32 ( 8933)
  SS BOND              : bond        0.00395 /  0.20 (    8)
  SS BOND              : angle       0.93043 /  0.47 (   16)
  hydrogen bonds       : bond        0.03720 /  2.48 (  258)
  hydrogen bonds       : angle       5.65017 /  3.98 (  750)
  link_NAG-ASN         : bond        0.01572 /  1.17 (    5)
  link_NAG-ASN         : angle       7.45817 /  3.85 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6399 (OUTLIER) cc_final: 0.6107 (t)
REVERT: B  381 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7503 (m)
REVERT: A  356 LYS cc_start: 0.7520 (tmtt) cc_final: 0.7059 (tttm)
REVERT: C   55 ARG cc_start: 0.1865 (mtt180) cc_final: 0.1004 (mmt180)
REVERT: C  147 LEU cc_start: 0.6876 (tp) cc_final: 0.6662 (tp)
REVERT: D  144 PHE cc_start: 0.5704 (p90) cc_final: 0.5405 (p90)
  outliers start: 34
  outliers final: 24
  residues processed: 115
  average time/residue: 0.0622
  time to fit residues: 9.5504
Evaluate side-chains
  109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  174 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.190674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.185384 restraints weight = 19573.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.183904 restraints weight = 30265.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.184040 restraints weight = 28816.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.183849 restraints weight = 24278.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.183836 restraints weight = 24409.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4442
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6570  Z= 0.141
  Angle     :  0.715  15.618   8964  Z= 0.338
  Chirality :  0.045   0.216   1037
  Planarity :  0.005   0.061   1133
  Dihedral  :  4.713  47.497    851
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 21.89 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.30), residues: 793
  helix:  1.24 (0.36), residues: 198
  sheet: -0.54 (0.33), residues: 253
  loop : -0.46 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  55 
 TYR   0.021   0.001   TYR B 254 
 PHE   0.026   0.002   PHE A 456 
 TRP   0.018   0.001   TRP C 100 
 HIS   0.010   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 6557)
  covalent geometry    : angle       0.66212 /  0.33 ( 8933)
  SS BOND              : bond        0.00429 /  0.22 (    8)
  SS BOND              : angle       0.89582 /  0.44 (   16)
  hydrogen bonds       : bond        0.03848 /  2.52 (  258)
  hydrogen bonds       : angle       5.48915 /  3.85 (  750)
  link_NAG-ASN         : bond        0.01691 /  1.11 (    5)
  link_NAG-ASN         : angle       6.59416 /  3.59 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 91
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6387 (OUTLIER) cc_final: 0.6134 (t)
REVERT: B  381 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7578 (m)
REVERT: C   55 ARG cc_start: 0.1664 (mtt180) cc_final: 0.0916 (mmt180)
REVERT: C  128 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4317 (pt)
REVERT: D  144 PHE cc_start: 0.5753 (p90) cc_final: 0.5498 (p90)
REVERT: D  168 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4728 (mm)
  outliers start: 44
  outliers final: 28
  residues processed: 118
  average time/residue: 0.0642
  time to fit residues: 9.9244
Evaluate side-chains
  113 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
A 440 ASN
C 165 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.187545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.183509 restraints weight = 18748.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.183053 restraints weight = 25080.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.183200 restraints weight = 23119.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183152 restraints weight = 18100.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.183219 restraints weight = 18136.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4476
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6570  Z= 0.204
  Angle     :  0.834  15.322   8964  Z= 0.399
  Chirality :  0.048   0.272   1037
  Planarity :  0.006   0.074   1133
  Dihedral  :  5.460  51.468    851
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 22.74 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.30), residues: 793
  helix:  0.56 (0.36), residues: 197
  sheet: -0.79 (0.34), residues: 243
  loop : -0.58 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 160 
 TYR   0.018   0.002   TYR B 254 
 PHE   0.028   0.002   PHE A 456 
 TRP   0.019   0.002   TRP C 100 
 HIS   0.014   0.002   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.20 ( 6557)
  covalent geometry    : angle       0.79040 /  0.39 ( 8933)
  SS BOND              : bond        0.00641 /  0.37 (    8)
  SS BOND              : angle       1.18591 /  0.59 (   16)
  hydrogen bonds       : bond        0.04166 /  2.81 (  258)
  hydrogen bonds       : angle       5.74417 /  4.03 (  750)
  link_NAG-ASN         : bond        0.01826 /  1.21 (    5)
  link_NAG-ASN         : angle       6.51627 /  3.53 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 89
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0533 (OUTLIER) cc_final: 0.0241 (pt)
REVERT: B  364 SER cc_start: 0.6583 (OUTLIER) cc_final: 0.6379 (t)
REVERT: C   55 ARG cc_start: 0.1727 (mtt180) cc_final: 0.1491 (mtt90)
REVERT: C  100 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.6444 (p-90)
REVERT: D  144 PHE cc_start: 0.6013 (p90) cc_final: 0.5693 (p90)
  outliers start: 47
  outliers final: 28
  residues processed: 118
  average time/residue: 0.0622
  time to fit residues: 9.5105
Evaluate side-chains
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  108 GLN
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.188818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.182749 restraints weight = 18869.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.180504 restraints weight = 26820.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 95)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.180366 restraints weight = 26990.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.180362 restraints weight = 27649.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.180356 restraints weight = 24987.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4612
moved from start:          0.4787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6570  Z= 0.139
  Angle     :  0.730  14.293   8964  Z= 0.344
  Chirality :  0.046   0.258   1037
  Planarity :  0.006   0.067   1133
  Dihedral  :  5.122  54.290    851
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 23.87 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.30), residues: 793
  helix:  0.79 (0.36), residues: 198
  sheet: -0.77 (0.33), residues: 251
  loop : -0.45 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.008   0.001   TYR D  66 
 PHE   0.022   0.002   PHE D 119 
 TRP   0.029   0.002   TRP B 450 
 HIS   0.012   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 6557)
  covalent geometry    : angle       0.68471 /  0.33 ( 8933)
  SS BOND              : bond        0.00445 /  0.24 (    8)
  SS BOND              : angle       1.01639 /  0.50 (   16)
  hydrogen bonds       : bond        0.03870 /  2.59 (  258)
  hydrogen bonds       : angle       5.44791 /  3.83 (  750)
  link_NAG-ASN         : bond        0.01589 /  1.06 (    5)
  link_NAG-ASN         : angle       6.18009 /  3.38 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 79
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6554 (OUTLIER) cc_final: 0.6332 (t)
REVERT: A  456 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7157 (t80)
REVERT: A  476 LYS cc_start: 0.4308 (tptp) cc_final: 0.2256 (ptmm)
REVERT: C   55 ARG cc_start: 0.1811 (mtt180) cc_final: 0.0870 (mmt180)
REVERT: C  100 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6612 (p-90)
REVERT: C  128 LEU cc_start: 0.4655 (OUTLIER) cc_final: 0.4285 (pt)
REVERT: D  144 PHE cc_start: 0.5869 (p90) cc_final: 0.5504 (p90)
  outliers start: 40
  outliers final: 27
  residues processed: 107
  average time/residue: 0.0612
  time to fit residues: 8.6353
Evaluate side-chains
  106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  113 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.189530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.184988 restraints weight = 18739.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.184532 restraints weight = 26177.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.184505 restraints weight = 25010.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.184159 restraints weight = 25413.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.184279 restraints weight = 22556.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4400
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6570  Z= 0.134
  Angle     :  0.718  14.075   8964  Z= 0.339
  Chirality :  0.046   0.268   1037
  Planarity :  0.005   0.068   1133
  Dihedral  :  5.034  55.368    851
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.73 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.30), residues: 793
  helix:  0.76 (0.36), residues: 198
  sheet: -0.69 (0.33), residues: 251
  loop : -0.41 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 346 
 TYR   0.007   0.001   TYR D  66 
 PHE   0.022   0.002   PHE D 119 
 TRP   0.062   0.002   TRP B 450 
 HIS   0.012   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 6557)
  covalent geometry    : angle       0.67444 /  0.33 ( 8933)
  SS BOND              : bond        0.00402 /  0.21 (    8)
  SS BOND              : angle       0.98878 /  0.49 (   16)
  hydrogen bonds       : bond        0.03762 /  2.55 (  258)
  hydrogen bonds       : angle       5.32833 /  3.76 (  750)
  link_NAG-ASN         : bond        0.01513 /  0.99 (    5)
  link_NAG-ASN         : angle       6.01827 /  3.30 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 79
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0827 (OUTLIER) cc_final: 0.0464 (pt)
REVERT: B  364 SER cc_start: 0.6683 (OUTLIER) cc_final: 0.6436 (t)
REVERT: A  456 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: A  476 LYS cc_start: 0.4196 (tptp) cc_final: 0.2319 (ptmm)
REVERT: C   55 ARG cc_start: 0.1932 (mtt180) cc_final: 0.0981 (mmt180)
REVERT: D  144 PHE cc_start: 0.5710 (p90) cc_final: 0.5356 (p90)
  outliers start: 38
  outliers final: 29
  residues processed: 108
  average time/residue: 0.0619
  time to fit residues: 8.9692
Evaluate side-chains
  111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  113 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 ASN
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.188826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.184048 restraints weight = 18793.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.183666 restraints weight = 28449.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.183719 restraints weight = 26453.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183441 restraints weight = 24204.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.183516 restraints weight = 22400.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.4519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4404
moved from start:          0.5227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6570  Z= 0.147
  Angle     :  0.734  13.992   8964  Z= 0.352
  Chirality :  0.046   0.271   1037
  Planarity :  0.006   0.069   1133
  Dihedral  :  5.086  55.999    851
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.16 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.30), residues: 793
  helix:  0.62 (0.36), residues: 198
  sheet: -0.59 (0.33), residues: 251
  loop : -0.48 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 153 
 TYR   0.010   0.001   TYR D 118 
 PHE   0.021   0.002   PHE D 119 
 TRP   0.087   0.002   TRP B 450 
 HIS   0.012   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 6557)
  covalent geometry    : angle       0.69244 /  0.34 ( 8933)
  SS BOND              : bond        0.00418 /  0.23 (    8)
  SS BOND              : angle       1.07608 /  0.53 (   16)
  hydrogen bonds       : bond        0.03870 /  2.69 (  258)
  hydrogen bonds       : angle       5.33832 /  3.77 (  750)
  link_NAG-ASN         : bond        0.01536 /  1.01 (    5)
  link_NAG-ASN         : angle       5.89799 /  3.22 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 81
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0820 (OUTLIER) cc_final: 0.0472 (pt)
REVERT: B  364 SER cc_start: 0.6775 (OUTLIER) cc_final: 0.6468 (t)
REVERT: A  343 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6438 (mm)
REVERT: A  456 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6966 (t80)
REVERT: C   55 ARG cc_start: 0.1845 (mtt180) cc_final: 0.1029 (mmt180)
REVERT: D  144 PHE cc_start: 0.5865 (p90) cc_final: 0.5486 (p90)
REVERT: D  168 ILE cc_start: 0.4787 (OUTLIER) cc_final: 0.4488 (mm)
  outliers start: 38
  outliers final: 29
  residues processed: 108
  average time/residue: 0.0630
  time to fit residues: 9.0087
Evaluate side-chains
  107 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  168 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.189402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.184831 restraints weight = 18546.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.184350 restraints weight = 28171.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.184190 restraints weight = 28235.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183817 restraints weight = 27653.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183828 restraints weight = 26929.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.4518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4415
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6570  Z= 0.145
  Angle     :  0.756  14.063   8964  Z= 0.364
  Chirality :  0.046   0.272   1037
  Planarity :  0.006   0.069   1133
  Dihedral  :  5.067  57.216    851
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.15 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.30), residues: 793
  helix:  0.68 (0.36), residues: 198
  sheet: -0.54 (0.33), residues: 251
  loop : -0.50 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 153 
 TYR   0.007   0.001   TYR D  66 
 PHE   0.021   0.002   PHE D 119 
 TRP   0.077   0.002   TRP B 450 
 HIS   0.012   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 6557)
  covalent geometry    : angle       0.71692 /  0.36 ( 8933)
  SS BOND              : bond        0.00375 /  0.20 (    8)
  SS BOND              : angle       1.08496 /  0.54 (   16)
  hydrogen bonds       : bond        0.03842 /  2.61 (  258)
  hydrogen bonds       : angle       5.29962 /  3.77 (  750)
  link_NAG-ASN         : bond        0.01481 /  0.97 (    5)
  link_NAG-ASN         : angle       5.81313 /  3.19 (   15)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0773 (OUTLIER) cc_final: 0.0424 (pt)
REVERT: B  364 SER cc_start: 0.6822 (OUTLIER) cc_final: 0.6505 (t)
REVERT: A  343 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6320 (mm)
REVERT: A  456 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.7012 (t80)
REVERT: C   55 ARG cc_start: 0.1877 (mtt180) cc_final: 0.0974 (mmt180)
REVERT: D  144 PHE cc_start: 0.5843 (p90) cc_final: 0.5482 (p90)
  outliers start: 35
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0632
  time to fit residues: 8.1631
Evaluate side-chains
  104 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  113 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0980
   chunk 72 optimal weight:    0.0970
   chunk 0 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 250 ASN
D  69 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.188185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.181439 restraints weight = 18640.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.180849 restraints weight = 24764.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.181035 restraints weight = 23279.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.180614 restraints weight = 23007.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.180765 restraints weight = 21162.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4579
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6570  Z= 0.173
  Angle     :  0.784  14.078   8964  Z= 0.379
  Chirality :  0.047   0.272   1037
  Planarity :  0.006   0.068   1133
  Dihedral  :  5.314  58.550    851
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.73 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.30), residues: 793
  helix:  0.56 (0.36), residues: 198
  sheet: -0.55 (0.33), residues: 246
  loop : -0.53 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 346 
 TYR   0.010   0.001   TYR A 466 
 PHE   0.021   0.002   PHE D 119 
 TRP   0.088   0.003   TRP B 450 
 HIS   0.013   0.002   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 ( 6557)
  covalent geometry    : angle       0.74820 /  0.37 ( 8933)
  SS BOND              : bond        0.00422 /  0.21 (    8)
  SS BOND              : angle       1.06751 /  0.52 (   16)
  hydrogen bonds       : bond        0.03982 /  2.75 (  258)
  hydrogen bonds       : angle       5.42285 /  3.84 (  750)
  link_NAG-ASN         : bond        0.01645 /  1.08 (    5)
  link_NAG-ASN         : angle       5.72430 /  3.09 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 946.20 seconds
wall clock time: 17 minutes 4.93 seconds (1024.93 seconds total)