Starting phenix.real_space_refine
on Tue Mar  3 13:15:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pag_13269/03_2026/7pag_13269.map"
  }
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 971 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      28      5.16       5
     C    2504      2.51       5
     N     746      2.21       5
     O     759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4040
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4023
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 23, 'TRANS': 485}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 17
          Unusual residues: {' CA': 3, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.01, per 1000 atoms: 0.25
  Number of scatterers: 4040
  At special positions: 0
  Unit cell: (91.12, 71.02, 171.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      28     16.00
     O     759      8.00
     N     746      7.00
     C    2504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  30 " - pdb=" SG  CYS A  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 380 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 396 " - pdb=" SG  CYS A 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 509 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 533 " 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 A 604 " - " ASN A 204 "
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 129.0 milliseconds
  

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      15.1% alpha, 54.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 189 through 199
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 4.372A  pdb=" N   HIS A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 217 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 312
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.726A  pdb=" N   PHE A 324 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 346 through 349
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 356 through 373
      removed outlier: 3.773A  pdb=" N   GLN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ALA A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TRP A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 3.564A  pdb=" N   HIS A 221 " --> pdb=" O   MET A  47 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 134
      removed outlier: 10.294A  pdb=" N   PHE A 180 " --> pdb=" O   PRO A  96 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   SER A  98 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   TYR A 178 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A 100 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   MET A 142 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 264 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 144 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLN A 262 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   GLU A 260 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   GLY A 148 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ASN A 258 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 256 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   CYS A 256 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS A 152 " --> pdb=" O   GLY A 254 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   GLY A 254 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A 154 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   GLU A 252 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   PHE A 156 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ALA A 158 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU A 248 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   LYS A 160 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ASN A 246 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR A 162 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   THR A 244 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   ASP A 164 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   TYR A 166 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR A 240 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   PHE A 168 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU A 238 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER A 170 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   THR A 236 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   THR A 172 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL A 234 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   GLU A 174 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   GLY A 230 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   SER A 341 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   VAL A 226 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP A 339 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
      removed outlier: 4.348A  pdb=" N   THR A  73 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.182A  pdb=" N   PHE A 421 " --> pdb=" O   TRP A 460 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   VAL A 418 " --> pdb=" O   HIS A 521 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   HIS A 521 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   ASN A 420 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER A 519 " --> pdb=" O   ASN A 420 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 470
      removed outlier: 5.188A  pdb=" N   ASP A 465 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL A 418 " --> pdb=" O   ASP A 465 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLU A 467 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 416 " --> pdb=" O   GLU A 467 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS A 523 " --> pdb=" O   HIS A 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448
      removed outlier: 6.633A  pdb=" N   LEU A 477 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ASP A 497 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 479 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER A 495 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 481 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP A 491 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    405 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: 0.51

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 669
        1.32 -     1.45: 1180
        1.45 -     1.58: 2251
        1.58 -     1.71: 0
        1.71 -     1.84: 36
  Bond restraints: 4136
  Sorted by residual:
  bond pdb=" C7  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" C1  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.504 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" C5  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" C2  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.439  1.499 -0.060 2.00e-02 2.50e+03 9.08e+00
  bond pdb=" C3  NAG A 604 "
       pdb=" O3  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.403  1.453 -0.050 2.00e-02 2.50e+03 6.19e+00
  ... (remaining 4131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 5355
        1.53 -     3.06: 197
        3.06 -     4.58: 39
        4.58 -     6.11: 19
        6.11 -     7.64: 1
  Bond angle restraints: 5611
  Sorted by residual:
  angle pdb=" N   ARG A 298 "
        pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     109.52  101.88    7.64 1.55e+00 4.16e-01 2.43e+01
  angle pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
        pdb=" O   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     121.44  116.82    4.62 1.17e+00 7.31e-01 1.56e+01
  angle pdb=" N   ASP A  82 "
        pdb=" CA  ASP A  82 "
        pdb=" C   ASP A  82 "
      ideal   model   delta    sigma   weight residual
     111.71  106.85    4.86 1.34e+00 5.57e-01 1.32e+01
  angle pdb=" N   VAL A 451 "
        pdb=" CA  VAL A 451 "
        pdb=" C   VAL A 451 "
      ideal   model   delta    sigma   weight residual
     107.37  111.93   -4.56 1.48e+00 4.57e-01 9.49e+00
  angle pdb=" C   CYS A 396 "
        pdb=" N   GLN A 397 "
        pdb=" CA  GLN A 397 "
      ideal   model   delta    sigma   weight residual
     121.54  126.90   -5.36 1.91e+00 2.74e-01 7.87e+00
  ... (remaining 5606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 2246
       17.11 -    34.22: 203
       34.22 -    51.33: 45
       51.33 -    68.44: 7
       68.44 -    85.55: 7
  Dihedral angle restraints: 2508
    sinusoidal: 1030
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CB  CYS A 376 "
           pdb=" SG  CYS A 376 "
           pdb=" SG  CYS A 392 "
           pdb=" CB  CYS A 392 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -4.35  -81.65     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS A 396 "
           pdb=" SG  CYS A 396 "
           pdb=" SG  CYS A 406 "
           pdb=" CB  CYS A 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.15  -53.15     1      1.00e+01 1.00e-02 3.84e+01
  dihedral pdb=" CA  LEU A 359 "
           pdb=" C   LEU A 359 "
           pdb=" N   ARG A 360 "
           pdb=" CA  ARG A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 2505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 370
       0.034 -    0.068: 156
       0.068 -    0.101: 48
       0.101 -    0.135: 26
       0.135 -    0.169: 4
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CA  ARG A 298 "
            pdb=" N   ARG A 298 "
            pdb=" C   ARG A 298 "
            pdb=" CB  ARG A 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  GLU A 446 "
            pdb=" N   GLU A 446 "
            pdb=" C   GLU A 446 "
            pdb=" CB  GLU A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 601 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 499 "    0.050 5.00e-02 4.00e+02   7.67e-02 9.42e+00
        pdb=" N   PRO A 500 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  95 "   -0.050 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO A  96 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 407 "    0.041 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 408 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.034 5.00e-02 4.00e+02
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 184
        2.72 -     3.27: 3973
        3.27 -     3.81: 6105
        3.81 -     4.36: 6879
        4.36 -     4.90: 12259
  Nonbonded interactions: 29400
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 320 "
            pdb=" OE1 GLN A 323 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   TYR A 366 "
            pdb=" OG  SER A 369 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OH  TYR A 366 "
            pdb=" NH1 ARG A 370 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OE2 GLU A 395 "
            pdb=" OG  SER A 399 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 361 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.247 3.040
  ... (remaining 29395 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.880
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5782
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   0.117   4146  Z= 0.232
  Angle     :  0.752   7.641   5632  Z= 0.413
  Chirality :  0.046   0.169    604
  Planarity :  0.006   0.077    738
  Dihedral  : 13.809  85.555   1525
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.35), residues: 505
  helix: -1.61 (0.67), residues: 55
  sheet:  0.15 (0.33), residues: 207
  loop : -2.22 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 422 
 TYR   0.012   0.001   TYR A 437 
 PHE   0.016   0.002   PHE A 447 
 TRP   0.026   0.002   TRP A 327 
 HIS   0.003   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 4136)
  covalent geometry    : angle       0.74596 ( 5611)
  SS BOND              : bond        0.00212 (    9)
  SS BOND              : angle       1.81967 (   18)
  hydrogen bonds       : bond        0.16793 (  143)
  hydrogen bonds       : angle       7.28566 (  405)
  link_NAG-ASN         : bond        0.00159 (    1)
  link_NAG-ASN         : angle       1.14799 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 LEU cc_start: 0.8991 (tp) cc_final: 0.8630 (mp)
REVERT: A  231 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7177 (ttt180)
REVERT: A  479 VAL cc_start: 0.9503 (t) cc_final: 0.9154 (p)
REVERT: A  518 PHE cc_start: 0.8358 (p90) cc_final: 0.8104 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0946
  time to fit residues: 10.4659
Evaluate side-chains
  45 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.0020
   chunk 48 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.1996

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5576 r_free = 0.5576 target = 0.384069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5537 r_free = 0.5537 target = 0.272811 restraints weight = 4292.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.5589 r_free = 0.5589 target = 0.200584 restraints weight = 2578.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.5589 r_free = 0.5589 target = 0.198046 restraints weight = 3875.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5589 r_free = 0.5589 target = 0.197599 restraints weight = 3993.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.5589 r_free = 0.5589 target = 0.196229 restraints weight = 3407.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.5189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4146  Z= 0.225
  Angle     :  0.744   8.352   5632  Z= 0.395
  Chirality :  0.048   0.150    604
  Planarity :  0.006   0.058    738
  Dihedral  :  5.392  20.955    579
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.59 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.35), residues: 505
  helix: -0.12 (0.68), residues: 53
  sheet: -0.69 (0.33), residues: 203
  loop : -2.11 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 360 
 TYR   0.016   0.002   TYR A 166 
 PHE   0.011   0.002   PHE A 315 
 TRP   0.032   0.002   TRP A 128 
 HIS   0.009   0.002   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 4136)
  covalent geometry    : angle       0.74054 ( 5611)
  SS BOND              : bond        0.00580 (    9)
  SS BOND              : angle       1.41733 (   18)
  hydrogen bonds       : bond        0.03210 (  143)
  hydrogen bonds       : angle       6.59002 (  405)
  link_NAG-ASN         : bond        0.00136 (    1)
  link_NAG-ASN         : angle       1.39975 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7675 (t)
REVERT: A  171 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6037 (t0)
REVERT: A  222 PHE cc_start: 0.8764 (p90) cc_final: 0.8118 (p90)
REVERT: A  231 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7444 (ttt90)
REVERT: A  366 TYR cc_start: 0.8258 (t80) cc_final: 0.7737 (t80)
REVERT: A  479 VAL cc_start: 0.9583 (t) cc_final: 0.9106 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0842
  time to fit residues: 6.9424
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    0.7980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5561 r_free = 0.5561 target = 0.384283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5525 r_free = 0.5525 target = 0.273296 restraints weight = 4288.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 113)---------------|
| r_work = 0.5580 r_free = 0.5580 target = 0.206430 restraints weight = 2628.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 84)----------------|
| r_work = 0.5580 r_free = 0.5580 target = 0.204109 restraints weight = 4038.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.5579 r_free = 0.5579 target = 0.202685 restraints weight = 4260.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5579 r_free = 0.5579 target = 0.202109 restraints weight = 4052.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.5194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4146  Z= 0.170
  Angle     :  0.704   9.655   5632  Z= 0.359
  Chirality :  0.046   0.147    604
  Planarity :  0.005   0.050    738
  Dihedral  :  4.825  16.847    579
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.24 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.36), residues: 505
  helix: -0.08 (0.70), residues: 59
  sheet: -0.74 (0.34), residues: 198
  loop : -2.11 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 478 
 TYR   0.009   0.001   TYR A 275 
 PHE   0.010   0.001   PHE A 168 
 TRP   0.032   0.002   TRP A 482 
 HIS   0.005   0.001   HIS A 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4136)
  covalent geometry    : angle       0.69892 ( 5611)
  SS BOND              : bond        0.00679 (    9)
  SS BOND              : angle       1.57126 (   18)
  hydrogen bonds       : bond        0.03127 (  143)
  hydrogen bonds       : angle       5.97654 (  405)
  link_NAG-ASN         : bond        0.00158 (    1)
  link_NAG-ASN         : angle       1.40439 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.8097 (m-40) cc_final: 0.7837 (t0)
REVERT: A  163 GLN cc_start: 0.7715 (pt0) cc_final: 0.7363 (tm-30)
REVERT: A  231 ARG cc_start: 0.7715 (ttm170) cc_final: 0.7461 (ttt180)
REVERT: A  372 ARG cc_start: 0.7251 (ppt170) cc_final: 0.6833 (ppt170)
REVERT: A  464 MET cc_start: 0.7024 (tpp) cc_final: 0.6700 (tpp)
REVERT: A  482 TRP cc_start: 0.7922 (m100) cc_final: 0.7606 (m100)
  outliers start: 6
  outliers final: 2
  residues processed: 52
  average time/residue: 0.0956
  time to fit residues: 5.9461
Evaluate side-chains
  41 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5510 r_free = 0.5510 target = 0.374631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5452 r_free = 0.5452 target = 0.257057 restraints weight = 4354.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5481 r_free = 0.5481 target = 0.198159 restraints weight = 2703.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 77)----------------|
| r_work = 0.5478 r_free = 0.5478 target = 0.188398 restraints weight = 4641.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 75)----------------|
| r_work = 0.5476 r_free = 0.5476 target = 0.186245 restraints weight = 4970.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.5479 r_free = 0.5479 target = 0.184230 restraints weight = 5095.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.5104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.5415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4146  Z= 0.230
  Angle     :  0.734  10.147   5632  Z= 0.390
  Chirality :  0.048   0.297    604
  Planarity :  0.005   0.050    738
  Dihedral  :  5.272  17.592    579
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.98 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.36), residues: 505
  helix: -0.35 (0.69), residues: 64
  sheet: -1.54 (0.34), residues: 208
  loop : -2.10 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  86 
 TYR   0.015   0.002   TYR A 275 
 PHE   0.021   0.002   PHE A 518 
 TRP   0.016   0.001   TRP A 482 
 HIS   0.005   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 4136)
  covalent geometry    : angle       0.72041 ( 5611)
  SS BOND              : bond        0.00839 (    9)
  SS BOND              : angle       2.55931 (   18)
  hydrogen bonds       : bond        0.03156 (  143)
  hydrogen bonds       : angle       6.62474 (  405)
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       1.27860 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8115 (m-30) cc_final: 0.7531 (t0)
REVERT: A  155 ASN cc_start: 0.8423 (m-40) cc_final: 0.8111 (t0)
REVERT: A  163 GLN cc_start: 0.7920 (pt0) cc_final: 0.7154 (tm-30)
REVERT: A  169 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7757 (p0)
REVERT: A  177 MET cc_start: 0.7647 (mmm) cc_final: 0.7427 (mmm)
REVERT: A  231 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7530 (ttt90)
REVERT: A  251 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6431 (t70)
REVERT: A  372 ARG cc_start: 0.7544 (ppt170) cc_final: 0.7116 (ppt170)
REVERT: A  464 MET cc_start: 0.7122 (tpp) cc_final: 0.6548 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0923
  time to fit residues: 6.7468
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 6 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0170
   chunk 24 optimal weight:    0.0270
   chunk 36 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.6280

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

Flipped N/Q/H residues before XYZ refinement:
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5510 r_free = 0.5510 target = 0.376627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5464 r_free = 0.5464 target = 0.260674 restraints weight = 4337.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 95)----------------|
| r_work = 0.5499 r_free = 0.5499 target = 0.189981 restraints weight = 2619.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 74)----------------|
| r_work = 0.5496 r_free = 0.5496 target = 0.186001 restraints weight = 3895.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.5497 r_free = 0.5497 target = 0.184434 restraints weight = 4391.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.5498 r_free = 0.5498 target = 0.182977 restraints weight = 4207.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.5102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.5823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4146  Z= 0.180
  Angle     :  0.743  11.202   5632  Z= 0.385
  Chirality :  0.048   0.369    604
  Planarity :  0.005   0.050    738
  Dihedral  :  4.855  17.945    579
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.35 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.36), residues: 505
  helix: -0.43 (0.68), residues: 64
  sheet: -1.46 (0.35), residues: 198
  loop : -2.12 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  86 
 TYR   0.010   0.001   TYR A 275 
 PHE   0.011   0.001   PHE A 156 
 TRP   0.031   0.002   TRP A 482 
 HIS   0.006   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4136)
  covalent geometry    : angle       0.72303 ( 5611)
  SS BOND              : bond        0.01259 (    9)
  SS BOND              : angle       3.10396 (   18)
  hydrogen bonds       : bond        0.02987 (  143)
  hydrogen bonds       : angle       6.11726 (  405)
  link_NAG-ASN         : bond        0.00124 (    1)
  link_NAG-ASN         : angle       1.29154 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.6151 (tpt90) cc_final: 0.5888 (ttp80)
REVERT: A  163 GLN cc_start: 0.7758 (pt0) cc_final: 0.7356 (tm-30)
REVERT: A  231 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7420 (ttt90)
REVERT: A  251 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7015 (t70)
REVERT: A  372 ARG cc_start: 0.7704 (ppt170) cc_final: 0.7344 (ppt170)
REVERT: A  464 MET cc_start: 0.7318 (tpp) cc_final: 0.6537 (tpp)
REVERT: A  477 LEU cc_start: 0.9151 (tt) cc_final: 0.8732 (mt)
REVERT: A  488 TRP cc_start: 0.5002 (p90) cc_final: 0.3613 (t60)
  outliers start: 9
  outliers final: 4
  residues processed: 52
  average time/residue: 0.1020
  time to fit residues: 6.3893
Evaluate side-chains
  47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 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 = 0.5504 r_free = 0.5504 target = 0.379727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5468 r_free = 0.5468 target = 0.263956 restraints weight = 4463.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.5501 r_free = 0.5501 target = 0.202839 restraints weight = 3046.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 76)----------------|
| r_work = 0.5498 r_free = 0.5498 target = 0.198947 restraints weight = 4445.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.5498 r_free = 0.5498 target = 0.197949 restraints weight = 4079.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 65)----------------|
| r_work = 0.5499 r_free = 0.5499 target = 0.196249 restraints weight = 3938.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.5127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
moved from start:          0.6098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4146  Z= 0.157
  Angle     :  0.765  16.792   5632  Z= 0.400
  Chirality :  0.045   0.178    604
  Planarity :  0.004   0.049    738
  Dihedral  :  4.836  22.568    579
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.72 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.36), residues: 505
  helix: -0.42 (0.68), residues: 64
  sheet: -1.40 (0.36), residues: 193
  loop : -2.11 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 478 
 TYR   0.008   0.001   TYR A 166 
 PHE   0.023   0.001   PHE A 518 
 TRP   0.025   0.001   TRP A 482 
 HIS   0.006   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4136)
  covalent geometry    : angle       0.73526 ( 5611)
  SS BOND              : bond        0.00866 (    9)
  SS BOND              : angle       3.80897 (   18)
  hydrogen bonds       : bond        0.03226 (  143)
  hydrogen bonds       : angle       6.06358 (  405)
  link_NAG-ASN         : bond        0.00138 (    1)
  link_NAG-ASN         : angle       1.22570 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7172 (t0)
REVERT: A  255 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.6578 (t0)
REVERT: A  464 MET cc_start: 0.7353 (tpp) cc_final: 0.6596 (tpp)
REVERT: A  477 LEU cc_start: 0.9132 (tt) cc_final: 0.8778 (mt)
REVERT: A  488 TRP cc_start: 0.5282 (p90) cc_final: 0.3693 (t60)
  outliers start: 10
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0897
  time to fit residues: 5.9652
Evaluate side-chains
  46 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 47 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 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 = 0.5504 r_free = 0.5504 target = 0.376774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5463 r_free = 0.5463 target = 0.258703 restraints weight = 4435.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5499 r_free = 0.5499 target = 0.205395 restraints weight = 2887.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.5495 r_free = 0.5495 target = 0.191133 restraints weight = 4350.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 75)----------------|
| r_work = 0.5495 r_free = 0.5495 target = 0.188455 restraints weight = 4150.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.5496 r_free = 0.5496 target = 0.186983 restraints weight = 4349.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.5120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.6336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4146  Z= 0.168
  Angle     :  0.792  17.910   5632  Z= 0.411
  Chirality :  0.049   0.340    604
  Planarity :  0.004   0.049    738
  Dihedral  :  4.702  18.375    579
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.26 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.35), residues: 505
  helix: -0.66 (0.65), residues: 64
  sheet: -1.38 (0.35), residues: 198
  loop : -2.03 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 360 
 TYR   0.011   0.001   TYR A 275 
 PHE   0.020   0.001   PHE A 156 
 TRP   0.034   0.002   TRP A 482 
 HIS   0.006   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4136)
  covalent geometry    : angle       0.75942 ( 5611)
  SS BOND              : bond        0.00719 (    9)
  SS BOND              : angle       4.03427 (   18)
  hydrogen bonds       : bond        0.03085 (  143)
  hydrogen bonds       : angle       6.08665 (  405)
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       1.19479 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7137 (t0)
REVERT: A  276 LYS cc_start: 0.8435 (mttt) cc_final: 0.7614 (tmtt)
REVERT: A  372 ARG cc_start: 0.6971 (ppt170) cc_final: 0.6752 (pmt-80)
REVERT: A  464 MET cc_start: 0.7409 (tpp) cc_final: 0.6617 (tpp)
REVERT: A  477 LEU cc_start: 0.9172 (tt) cc_final: 0.8769 (mt)
REVERT: A  488 TRP cc_start: 0.5464 (p90) cc_final: 0.3750 (t60)
  outliers start: 14
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1012
  time to fit residues: 6.8663
Evaluate side-chains
  51 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 15 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5467 r_free = 0.5467 target = 0.368642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5409 r_free = 0.5409 target = 0.248873 restraints weight = 4337.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.192103 restraints weight = 3145.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 180)---------------|
| r_work = 0.5391 r_free = 0.5391 target = 0.179005 restraints weight = 4656.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.5392 r_free = 0.5392 target = 0.176161 restraints weight = 5650.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5392 r_free = 0.5392 target = 0.175046 restraints weight = 5628.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.5048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.6718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4146  Z= 0.216
  Angle     :  0.949  26.275   5632  Z= 0.485
  Chirality :  0.049   0.308    604
  Planarity :  0.005   0.048    738
  Dihedral  :  5.096  21.013    579
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.63 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.36), residues: 505
  helix: -0.74 (0.66), residues: 64
  sheet: -1.67 (0.34), residues: 208
  loop : -2.02 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  70 
 TYR   0.015   0.002   TYR A 166 
 PHE   0.023   0.002   PHE A 518 
 TRP   0.027   0.002   TRP A 482 
 HIS   0.007   0.001   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4136)
  covalent geometry    : angle       0.91684 ( 5611)
  SS BOND              : bond        0.01216 (    9)
  SS BOND              : angle       4.40377 (   18)
  hydrogen bonds       : bond        0.03532 (  143)
  hydrogen bonds       : angle       6.75721 (  405)
  link_NAG-ASN         : bond        0.00111 (    1)
  link_NAG-ASN         : angle       1.17368 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6746 (t70)
REVERT: A  372 ARG cc_start: 0.7317 (ppt170) cc_final: 0.7114 (pmt-80)
REVERT: A  464 MET cc_start: 0.7368 (tpp) cc_final: 0.6567 (tpp)
REVERT: A  477 LEU cc_start: 0.9153 (tt) cc_final: 0.8796 (mt)
REVERT: A  488 TRP cc_start: 0.5640 (p90) cc_final: 0.3509 (t60)
  outliers start: 13
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1013
  time to fit residues: 6.4196
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 MET
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5467 r_free = 0.5467 target = 0.371569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5420 r_free = 0.5420 target = 0.251632 restraints weight = 4421.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5433 r_free = 0.5433 target = 0.185202 restraints weight = 2818.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 95)----------------|
| r_work = 0.5424 r_free = 0.5424 target = 0.175840 restraints weight = 3897.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 81)----------------|
| r_work = 0.5426 r_free = 0.5426 target = 0.172738 restraints weight = 4141.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.5427 r_free = 0.5427 target = 0.170397 restraints weight = 4641.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.5045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.6886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4146  Z= 0.183
  Angle     :  0.910  27.690   5632  Z= 0.464
  Chirality :  0.051   0.447    604
  Planarity :  0.004   0.048    738
  Dihedral  :  4.862  17.377    579
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.18 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.36), residues: 505
  helix: -0.72 (0.66), residues: 64
  sheet: -1.57 (0.34), residues: 208
  loop : -1.93 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  70 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.021   0.002   PHE A 156 
 TRP   0.024   0.002   TRP A 482 
 HIS   0.005   0.001   HIS A 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4136)
  covalent geometry    : angle       0.87924 ( 5611)
  SS BOND              : bond        0.01147 (    9)
  SS BOND              : angle       4.24601 (   18)
  hydrogen bonds       : bond        0.03419 (  143)
  hydrogen bonds       : angle       6.48084 (  405)
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       1.16408 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7279 (t70)
REVERT: A  276 LYS cc_start: 0.8445 (mttt) cc_final: 0.7642 (tptp)
REVERT: A  372 ARG cc_start: 0.7301 (ppt170) cc_final: 0.7098 (pmt-80)
REVERT: A  464 MET cc_start: 0.7419 (tpp) cc_final: 0.6656 (tpp)
REVERT: A  477 LEU cc_start: 0.9160 (tt) cc_final: 0.8776 (mt)
REVERT: A  488 TRP cc_start: 0.5290 (p90) cc_final: 0.3459 (t60)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1020
  time to fit residues: 6.1751
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5418 r_free = 0.5418 target = 0.360203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5317 r_free = 0.5317 target = 0.185366 restraints weight = 4451.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5298 r_free = 0.5298 target = 0.181931 restraints weight = 7403.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5301 r_free = 0.5301 target = 0.177255 restraints weight = 5981.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5293 r_free = 0.5293 target = 0.174032 restraints weight = 5950.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.172063 restraints weight = 5502.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.7375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4146  Z= 0.321
  Angle     :  1.046  27.147   5632  Z= 0.546
  Chirality :  0.055   0.447    604
  Planarity :  0.006   0.048    738
  Dihedral  :  6.045  21.276    579
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.18 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.36), residues: 505
  helix: -0.75 (0.66), residues: 64
  sheet: -2.43 (0.32), residues: 208
  loop : -1.96 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  86 
 TYR   0.026   0.003   TYR A 166 
 PHE   0.027   0.003   PHE A 518 
 TRP   0.028   0.002   TRP A 482 
 HIS   0.014   0.002   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 4136)
  covalent geometry    : angle       1.01978 ( 5611)
  SS BOND              : bond        0.01318 (    9)
  SS BOND              : angle       4.24161 (   18)
  hydrogen bonds       : bond        0.04521 (  143)
  hydrogen bonds       : angle       7.98003 (  405)
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       1.10906 (    3)

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8029 (tt0) cc_final: 0.7321 (tm-30)
REVERT: A  464 MET cc_start: 0.7548 (tpp) cc_final: 0.6733 (tpp)
REVERT: A  477 LEU cc_start: 0.9164 (tt) cc_final: 0.8875 (mt)
REVERT: A  488 TRP cc_start: 0.5652 (p90) cc_final: 0.3438 (t60)
  outliers start: 10
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0955
  time to fit residues: 5.7812
Evaluate side-chains
  48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5453 r_free = 0.5453 target = 0.368257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.241850 restraints weight = 4431.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5396 r_free = 0.5396 target = 0.196845 restraints weight = 4128.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.5384 r_free = 0.5384 target = 0.186181 restraints weight = 5196.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 100)---------------|
| r_work = 0.5382 r_free = 0.5382 target = 0.180607 restraints weight = 4735.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.5383 r_free = 0.5383 target = 0.178776 restraints weight = 5048.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.5051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.7383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4146  Z= 0.197
  Angle     :  0.938  25.676   5632  Z= 0.479
  Chirality :  0.052   0.417    604
  Planarity :  0.005   0.049    738
  Dihedral  :  5.341  22.302    579
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.86 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.36), residues: 505
  helix: -1.00 (0.63), residues: 64
  sheet: -2.11 (0.33), residues: 208
  loop : -1.88 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  86 
 TYR   0.013   0.002   TYR A 366 
 PHE   0.023   0.002   PHE A 156 
 TRP   0.032   0.002   TRP A 327 
 HIS   0.005   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4136)
  covalent geometry    : angle       0.90872 ( 5611)
  SS BOND              : bond        0.01055 (    9)
  SS BOND              : angle       4.18004 (   18)
  hydrogen bonds       : bond        0.03726 (  143)
  hydrogen bonds       : angle       6.95981 (  405)
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       1.18054 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.45 seconds
wall clock time: 18 minutes 34.31 seconds (1114.31 seconds total)