Starting phenix.real_space_refine
on Fri Aug 22 17:31:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_27888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_27888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_27888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_27888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e4c_27888/08_2025/8e4c_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6
          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 dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.72, per 1000 atoms: 0.27
  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: 0.49
  Conformation dependent library (CDL) restraints added in 320.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.69

  Time building geometry restraints manager: 0.67 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: 3481
       17.92 -    35.85: 379
       35.85 -    53.77: 107
       53.77 -    71.70: 22
       71.70 -    89.62: 7
  Dihedral angle restraints: 3996
    sinusoidal: 1661
      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 3993 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:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.960
  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:0.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4891
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  : 16.284  89.622   2454
  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 aren 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
  covalent geometry    : bond        0.00502 ( 6557)
  covalent geometry    : angle       0.83843 ( 8933)
  SS BOND              : bond        0.01155 (    8)
  SS BOND              : angle       1.47526 (   16)
  hydrogen bonds       : bond        0.20036 (  258)
  hydrogen bonds       : angle       9.50777 (  750)
  link_NAG-ASN         : bond        0.01638 (    5)
  link_NAG-ASN         : angle       3.00486 (   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  : 0.165 
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: 0.0913
  time to fit residues: 18.7755
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  : 0.234 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.189246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.184516 restraints weight = 18975.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.183786 restraints weight = 29849.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.183827 restraints weight = 28827.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.183766 restraints weight = 23417.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.183756 restraints weight = 23206.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.4521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4378
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6570  Z= 0.150
  Angle     :  0.715   9.728   8964  Z= 0.352
  Chirality :  0.049   0.285   1037
  Planarity :  0.006   0.075   1133
  Dihedral  :  6.579  61.232    966
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.89 %
    Favored  : 73.87 %
  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 aren not related in a simple way.
  whole: -0.31 (0.30), residues: 793
  helix:  1.29 (0.36), residues: 197
  sheet: -0.57 (0.34), residues: 252
  loop : -0.70 (0.34), residues: 344

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   0.020   0.002   PHE D 119 
 TRP   0.019   0.001   TRP C 100 
 HIS   0.013   0.002   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6557)
  covalent geometry    : angle       0.70349 ( 8933)
  SS BOND              : bond        0.00515 (    8)
  SS BOND              : angle       0.95769 (   16)
  hydrogen bonds       : bond        0.04397 (  258)
  hydrogen bonds       : angle       6.61084 (  750)
  link_NAG-ASN         : bond        0.01102 (    5)
  link_NAG-ASN         : angle       3.11371 (   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  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  351 VAL cc_start: 0.6833 (t) cc_final: 0.6614 (m)
REVERT: B  402 VAL cc_start: 0.7226 (m) cc_final: 0.7014 (m)
REVERT: B  409 SER cc_start: 0.6150 (p) cc_final: 0.5733 (m)
REVERT: C   55 ARG cc_start: 0.2113 (mtt180) cc_final: 0.1414 (mmt180)
REVERT: C   71 TRP cc_start: 0.4688 (m100) cc_final: 0.4436 (m100)
REVERT: C  147 LEU cc_start: 0.7048 (tp) cc_final: 0.6633 (tp)
REVERT: C  162 ARG cc_start: 0.1586 (ttp-110) cc_final: 0.0951 (mmt180)
REVERT: D  144 PHE cc_start: 0.5692 (p90) cc_final: 0.5371 (p90)
  outliers start: 30
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0804
  time to fit residues: 12.3248
Evaluate side-chains
  103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 VAL
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:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 27 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4617 r_free = 0.4617 target = 0.190397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.184397 restraints weight = 19286.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.183562 restraints weight = 33780.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.183722 restraints weight = 32366.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.183435 restraints weight = 26709.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.183593 restraints weight = 24162.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.4509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4435
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6570  Z= 0.147
  Angle     :  0.698  16.786   8964  Z= 0.338
  Chirality :  0.045   0.223   1037
  Planarity :  0.005   0.062   1133
  Dihedral  :  6.033  52.592    961
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 21.19 %
    Favored  : 72.88 %
  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 aren not related in a simple way.
  whole: -0.22 (0.30), residues: 793
  helix:  1.39 (0.36), residues: 199
  sheet: -0.57 (0.33), residues: 250
  loop : -0.62 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  79 
 TYR   0.021   0.001   TYR B 254 
 PHE   0.024   0.002   PHE A 456 
 TRP   0.018   0.001   TRP C 100 
 HIS   0.009   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6557)
  covalent geometry    : angle       0.65659 ( 8933)
  SS BOND              : bond        0.00436 (    8)
  SS BOND              : angle       1.07013 (   16)
  hydrogen bonds       : bond        0.03938 (  258)
  hydrogen bonds       : angle       5.98050 (  750)
  link_NAG-ASN         : bond        0.02982 (    5)
  link_NAG-ASN         : angle       5.73352 (   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
  135 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 93
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  351 VAL cc_start: 0.6842 (t) cc_final: 0.6624 (m)
REVERT: B  364 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.6151 (t)
REVERT: A  276 MET cc_start: 0.4840 (mmp) cc_final: 0.4425 (mmp)
REVERT: C   55 ARG cc_start: 0.1896 (mtt180) cc_final: 0.1182 (mmt180)
REVERT: C  147 LEU cc_start: 0.6948 (tp) cc_final: 0.6664 (tp)
REVERT: C  162 ARG cc_start: 0.1673 (ttp-110) cc_final: 0.0985 (mmt180)
REVERT: D  144 PHE cc_start: 0.5736 (p90) cc_final: 0.5427 (p90)
  outliers start: 42
  outliers final: 24
  residues processed: 120
  average time/residue: 0.0784
  time to fit residues: 12.2565
Evaluate side-chains
  105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  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 B residue  464 LEU
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  174 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0770
   chunk 49 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0970
   chunk 50 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0070
   chunk 58 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.2754

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
** 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 = 0.4634 r_free = 0.4634 target = 0.192242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.185274 restraints weight = 19326.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183163 restraints weight = 27904.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 80)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.182629 restraints weight = 28650.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.182558 restraints weight = 30298.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.182552 restraints weight = 29665.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.4484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4553
moved from start:          0.3550

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= 0.124
  Angle     :  0.723  18.569   8964  Z= 0.339
  Chirality :  0.045   0.237   1037
  Planarity :  0.005   0.059   1133
  Dihedral  :  6.223  57.280    958
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.92 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.32 %
    Favored  : 72.88 %
  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 aren not related in a simple way.
  whole: -0.05 (0.30), residues: 793
  helix:  1.42 (0.36), residues: 198
  sheet: -0.50 (0.33), residues: 253
  loop : -0.40 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 340 
 TYR   0.023   0.001   TYR B 254 
 PHE   0.020   0.001   PHE D 119 
 TRP   0.022   0.001   TRP B 297 
 HIS   0.009   0.001   HIS D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6557)
  covalent geometry    : angle       0.64233 ( 8933)
  SS BOND              : bond        0.00392 (    8)
  SS BOND              : angle       0.96574 (   16)
  hydrogen bonds       : bond        0.03728 (  258)
  hydrogen bonds       : angle       5.54195 (  750)
  link_NAG-ASN         : bond        0.01275 (    5)
  link_NAG-ASN         : angle       8.10202 (   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
  127 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 93
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6353 (OUTLIER) cc_final: 0.6072 (t)
REVERT: B  443 GLU cc_start: 0.6100 (pp20) cc_final: 0.5854 (pp20)
REVERT: A  276 MET cc_start: 0.4849 (mmp) cc_final: 0.4513 (mmp)
REVERT: A  356 LYS cc_start: 0.7511 (tmtt) cc_final: 0.6981 (tttm)
REVERT: C   55 ARG cc_start: 0.1891 (mtt180) cc_final: 0.1000 (mmt180)
REVERT: C   96 ARG cc_start: 0.7693 (ptt180) cc_final: 0.7255 (ptm160)
REVERT: D  144 PHE cc_start: 0.5708 (p90) cc_final: 0.5427 (p90)
  outliers start: 34
  outliers final: 22
  residues processed: 117
  average time/residue: 0.0801
  time to fit residues: 12.4080
Evaluate side-chains
  107 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  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  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  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  103 VAL
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7902

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

Flipped N/Q/H residues before XYZ refinement:
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**
** 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 = 0.4619 r_free = 0.4619 target = 0.191163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.184326 restraints weight = 19580.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.183442 restraints weight = 27658.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.183141 restraints weight = 29586.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.182830 restraints weight = 27637.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 75)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.182576 restraints weight = 27350.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4544
moved from start:          0.3820

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= 0.140
  Angle     :  0.722  17.464   8964  Z= 0.341
  Chirality :  0.046   0.223   1037
  Planarity :  0.005   0.059   1133
  Dihedral  :  5.732  57.936    956
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.74 %
    Favored  : 71.75 %
  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 aren not related in a simple way.
  whole: -0.18 (0.30), residues: 793
  helix:  1.16 (0.36), residues: 199
  sheet: -0.57 (0.33), residues: 255
  loop : -0.38 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  55 
 TYR   0.021   0.001   TYR B 254 
 PHE   0.029   0.002   PHE A 456 
 TRP   0.016   0.001   TRP C 100 
 HIS   0.010   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6557)
  covalent geometry    : angle       0.65997 ( 8933)
  SS BOND              : bond        0.00483 (    8)
  SS BOND              : angle       0.90619 (   16)
  hydrogen bonds       : bond        0.03781 (  258)
  hydrogen bonds       : angle       5.49092 (  750)
  link_NAG-ASN         : bond        0.01529 (    5)
  link_NAG-ASN         : angle       7.17430 (   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
  130 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6395 (OUTLIER) cc_final: 0.6137 (t)
REVERT: A  276 MET cc_start: 0.4814 (mmp) cc_final: 0.4471 (mmp)
REVERT: C   55 ARG cc_start: 0.1776 (mtt180) cc_final: 0.0841 (mmt180)
REVERT: C  128 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4377 (pt)
REVERT: D  118 TYR cc_start: 0.6336 (m-80) cc_final: 0.5954 (m-10)
REVERT: D  144 PHE cc_start: 0.5781 (p90) cc_final: 0.5427 (p90)
  outliers start: 39
  outliers final: 27
  residues processed: 117
  average time/residue: 0.0721
  time to fit residues: 10.9476
Evaluate side-chains
  109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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  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  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   42 LEU
Chi-restraints excluded: chain C residue   60 THR
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0020
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
A 440 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.191357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.184797 restraints weight = 19405.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 111)---------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.182513 restraints weight = 27021.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.182177 restraints weight = 28570.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.182084 restraints weight = 29273.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.182061 restraints weight = 30906.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4582
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6570  Z= 0.133
  Angle     :  0.722  16.681   8964  Z= 0.342
  Chirality :  0.045   0.258   1037
  Planarity :  0.005   0.084   1133
  Dihedral  :  5.508  55.577    956
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 23.73 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.30), residues: 793
  helix:  1.17 (0.35), residues: 197
  sheet: -0.56 (0.32), residues: 261
  loop : -0.34 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 160 
 TYR   0.020   0.001   TYR B 254 
 PHE   0.024   0.002   PHE A 395 
 TRP   0.015   0.001   TRP C 100 
 HIS   0.009   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6557)
  covalent geometry    : angle       0.66748 ( 8933)
  SS BOND              : bond        0.00377 (    8)
  SS BOND              : angle       0.80725 (   16)
  hydrogen bonds       : bond        0.03629 (  258)
  hydrogen bonds       : angle       5.24087 (  750)
  link_NAG-ASN         : bond        0.01494 (    5)
  link_NAG-ASN         : angle       6.76736 (   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
  120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.6149 (t)
REVERT: A  276 MET cc_start: 0.4871 (mmp) cc_final: 0.4495 (mmp)
REVERT: C   55 ARG cc_start: 0.1800 (mtt180) cc_final: 0.0796 (mmt180)
REVERT: C  128 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.4248 (pt)
REVERT: D  118 TYR cc_start: 0.6310 (m-80) cc_final: 0.5973 (m-10)
REVERT: D  138 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6768 (tt0)
  outliers start: 37
  outliers final: 27
  residues processed: 108
  average time/residue: 0.0724
  time to fit residues: 10.3330
Evaluate side-chains
  105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 B residue  464 LEU
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  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  168 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0170
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.0822

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
D  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.189455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.183078 restraints weight = 19467.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.181924 restraints weight = 26812.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 175)---------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.181338 restraints weight = 24650.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.180755 restraints weight = 29212.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.180749 restraints weight = 28237.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4619
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6570  Z= 0.156
  Angle     :  0.752  16.701   8964  Z= 0.357
  Chirality :  0.046   0.277   1037
  Planarity :  0.006   0.071   1133
  Dihedral  :  5.689  53.651    956
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 23.73 %
    Favored  : 70.34 %
  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 aren not related in a simple way.
  whole: -0.26 (0.30), residues: 793
  helix:  1.00 (0.36), residues: 198
  sheet: -0.51 (0.33), residues: 263
  loop : -0.45 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  55 
 TYR   0.018   0.001   TYR B 254 
 PHE   0.023   0.002   PHE A 395 
 TRP   0.030   0.002   TRP B 450 
 HIS   0.012   0.002   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6557)
  covalent geometry    : angle       0.69909 ( 8933)
  SS BOND              : bond        0.00456 (    8)
  SS BOND              : angle       1.07181 (   16)
  hydrogen bonds       : bond        0.03739 (  258)
  hydrogen bonds       : angle       5.39687 (  750)
  link_NAG-ASN         : bond        0.01619 (    5)
  link_NAG-ASN         : angle       6.78865 (   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
  127 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 85
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: B  364 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.6228 (t)
REVERT: A  456 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.7062 (t80)
REVERT: A  476 LYS cc_start: 0.4101 (tptp) cc_final: 0.2437 (ptmm)
REVERT: C   55 ARG cc_start: 0.1906 (mtt180) cc_final: 0.0959 (mmt-90)
REVERT: C  100 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.6274 (p-90)
REVERT: C  128 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4224 (pt)
REVERT: D  168 ILE cc_start: 0.4915 (OUTLIER) cc_final: 0.4683 (mm)
  outliers start: 42
  outliers final: 25
  residues processed: 109
  average time/residue: 0.0804
  time to fit residues: 11.5593
Evaluate side-chains
  106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 B residue  464 LEU
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  456 PHE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 LEU
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.189756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.185235 restraints weight = 18682.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.183376 restraints weight = 25519.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.183044 restraints weight = 30828.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.183044 restraints weight = 26585.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.183044 restraints weight = 26509.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4505
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6570  Z= 0.139
  Angle     :  0.736  16.226   8964  Z= 0.348
  Chirality :  0.046   0.288   1037
  Planarity :  0.005   0.061   1133
  Dihedral  :  5.630  53.417    956
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 23.73 %
    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 aren not related in a simple way.
  whole: -0.19 (0.30), residues: 793
  helix:  0.88 (0.36), residues: 198
  sheet: -0.44 (0.34), residues: 252
  loop : -0.33 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 346 
 TYR   0.018   0.001   TYR B 254 
 PHE   0.019   0.002   PHE A 395 
 TRP   0.021   0.002   TRP B 450 
 HIS   0.011   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6557)
  covalent geometry    : angle       0.68413 ( 8933)
  SS BOND              : bond        0.00443 (    8)
  SS BOND              : angle       0.94754 (   16)
  hydrogen bonds       : bond        0.03726 (  258)
  hydrogen bonds       : angle       5.36623 (  750)
  link_NAG-ASN         : bond        0.01569 (    5)
  link_NAG-ASN         : angle       6.61422 (   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
  121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 80
  time to evaluate  : 0.244 
Fit side-chains
REVERT: B  273 ILE cc_start: 0.0526 (OUTLIER) cc_final: 0.0203 (pt)
REVERT: B  364 SER cc_start: 0.6455 (OUTLIER) cc_final: 0.6237 (t)
REVERT: A  276 MET cc_start: 0.4813 (OUTLIER) cc_final: 0.4337 (mmp)
REVERT: A  456 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7105 (t80)
REVERT: A  476 LYS cc_start: 0.4341 (tptp) cc_final: 0.2498 (ptmm)
REVERT: C   55 ARG cc_start: 0.1828 (mtt180) cc_final: 0.0910 (mmt180)
REVERT: C  100 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.6229 (p-90)
REVERT: D  168 ILE cc_start: 0.4906 (mm) cc_final: 0.4596 (mm)
  outliers start: 41
  outliers final: 27
  residues processed: 106
  average time/residue: 0.0768
  time to fit residues: 10.6820
Evaluate side-chains
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  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 A residue  456 PHE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 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  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 44 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0770
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4605 r_free = 0.4605 target = 0.190322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.185630 restraints weight = 18901.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.185306 restraints weight = 29626.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.185292 restraints weight = 28275.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.185214 restraints weight = 24069.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.185311 restraints weight = 21268.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4371
moved from start:          0.4859

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     :  0.736  15.797   8964  Z= 0.350
  Chirality :  0.046   0.289   1037
  Planarity :  0.005   0.064   1133
  Dihedral  :  5.580  52.986    956
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 23.59 %
    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 aren not related in a simple way.
  whole: -0.14 (0.30), residues: 793
  helix:  0.78 (0.36), residues: 198
  sheet: -0.34 (0.34), residues: 252
  loop : -0.25 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 346 
 TYR   0.016   0.001   TYR B 254 
 PHE   0.020   0.002   PHE D 119 
 TRP   0.062   0.002   TRP B 450 
 HIS   0.011   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6557)
  covalent geometry    : angle       0.68768 ( 8933)
  SS BOND              : bond        0.00374 (    8)
  SS BOND              : angle       0.93046 (   16)
  hydrogen bonds       : bond        0.03713 (  258)
  hydrogen bonds       : angle       5.24717 (  750)
  link_NAG-ASN         : bond        0.01463 (    5)
  link_NAG-ASN         : angle       6.44859 (   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
  124 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0674 (OUTLIER) cc_final: 0.0323 (pt)
REVERT: A  276 MET cc_start: 0.4796 (OUTLIER) cc_final: 0.4287 (mmp)
REVERT: A  456 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6958 (t80)
REVERT: A  476 LYS cc_start: 0.4257 (tptp) cc_final: 0.2488 (ptmm)
REVERT: C   55 ARG cc_start: 0.1903 (mtt180) cc_final: 0.0866 (mmt180)
REVERT: C  100 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.6282 (p-90)
REVERT: D  168 ILE cc_start: 0.4807 (mm) cc_final: 0.4508 (mm)
  outliers start: 39
  outliers final: 28
  residues processed: 109
  average time/residue: 0.0753
  time to fit residues: 10.9216
Evaluate side-chains
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
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 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  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   37 SER
Chi-restraints excluded: chain C residue   42 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  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   69 HIS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0170
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.190255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.185796 restraints weight = 18678.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.185031 restraints weight = 25384.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.184573 restraints weight = 23785.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.184411 restraints weight = 27431.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.184377 restraints weight = 24586.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4439
moved from start:          0.5058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6570  Z= 0.139
  Angle     :  0.740  15.516   8964  Z= 0.353
  Chirality :  0.046   0.286   1037
  Planarity :  0.005   0.064   1133
  Dihedral  :  5.645  54.970    956
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.72 %
    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 aren not related in a simple way.
  whole: -0.05 (0.31), residues: 793
  helix:  0.90 (0.35), residues: 198
  sheet: -0.25 (0.34), residues: 252
  loop : -0.25 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 346 
 TYR   0.018   0.001   TYR B 254 
 PHE   0.022   0.002   PHE D 119 
 TRP   0.081   0.002   TRP B 450 
 HIS   0.011   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6557)
  covalent geometry    : angle       0.69264 ( 8933)
  SS BOND              : bond        0.00382 (    8)
  SS BOND              : angle       0.93641 (   16)
  hydrogen bonds       : bond        0.03711 (  258)
  hydrogen bonds       : angle       5.14931 (  750)
  link_NAG-ASN         : bond        0.01474 (    5)
  link_NAG-ASN         : angle       6.34983 (   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
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0640 (OUTLIER) cc_final: 0.0274 (pt)
REVERT: A  276 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.4315 (mmp)
REVERT: A  456 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6967 (t80)
REVERT: A  476 LYS cc_start: 0.4324 (tptp) cc_final: 0.2496 (ptmm)
REVERT: C   55 ARG cc_start: 0.2023 (mtt180) cc_final: 0.0947 (mmt180)
REVERT: D   88 VAL cc_start: 0.1480 (OUTLIER) cc_final: 0.1134 (p)
REVERT: D  168 ILE cc_start: 0.4894 (mm) cc_final: 0.4560 (mm)
  outliers start: 34
  outliers final: 27
  residues processed: 99
  average time/residue: 0.0854
  time to fit residues: 11.1159
Evaluate side-chains
  104 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 73
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
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 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  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  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   69 HIS
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0770
   chunk 56 optimal weight:    0.0670
   chunk 70 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.0078

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 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 = 0.188921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.184475 restraints weight = 18790.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.183426 restraints weight = 28643.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.183296 restraints weight = 31334.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.183270 restraints weight = 26799.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.183425 restraints weight = 23586.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4479
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6570  Z= 0.157
  Angle     :  0.769  15.445   8964  Z= 0.367
  Chirality :  0.047   0.280   1037
  Planarity :  0.006   0.064   1133
  Dihedral  :  5.928  57.882    956
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.58 %
    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 aren not related in a simple way.
  whole: -0.20 (0.30), residues: 793
  helix:  0.81 (0.36), residues: 198
  sheet: -0.31 (0.34), residues: 252
  loop : -0.40 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 346 
 TYR   0.017   0.001   TYR B 254 
 PHE   0.022   0.002   PHE D 119 
 TRP   0.056   0.002   TRP B 450 
 HIS   0.012   0.002   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6557)
  covalent geometry    : angle       0.72375 ( 8933)
  SS BOND              : bond        0.00394 (    8)
  SS BOND              : angle       1.01415 (   16)
  hydrogen bonds       : bond        0.03880 (  258)
  hydrogen bonds       : angle       5.34215 (  750)
  link_NAG-ASN         : bond        0.01626 (    5)
  link_NAG-ASN         : angle       6.38266 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1131.42 seconds
wall clock time: 20 minutes 13.75 seconds (1213.75 seconds total)