Starting phenix.real_space_refine
on Thu Jul 24 02:06:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_13269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_13269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_13269.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_13269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2025/7pag_13269.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.23, per 1000 atoms: 0.80
  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: 1.02
  Conformation dependent library (CDL) restraints added in 505.5 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: 0.45
  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: 1.03

  Time building geometry restraints manager: 1.23 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:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.700
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.710
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.026   0.002   TRP A 327 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.016   0.002   PHE A 447 
 TYR   0.012   0.001   TYR A 437 
 ARG   0.006   0.001   ARG A 422 

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

*********************** 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  : 0.428 
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: 0.7176 (ttt180)
REVERT: A  479 VAL cc_start: 0.9503 (t) cc_final: 0.9156 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2206
  time to fit residues: 24.4256
Evaluate side-chains
  48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
A 285 HIS
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5500 r_free = 0.5500 target = 0.361610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5397 r_free = 0.5397 target = 0.216727 restraints weight = 4469.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5349 r_free = 0.5349 target = 0.180535 restraints weight = 5600.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.5340 r_free = 0.5340 target = 0.172602 restraints weight = 5660.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.5062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.5032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.077   4146  Z= 0.465
  Angle     :  1.052  10.591   5632  Z= 0.575
  Chirality :  0.056   0.258    604
  Planarity :  0.009   0.092    738
  Dihedral  :  7.545  30.017    579
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 24.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 11.42 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.35), residues: 505
  helix: -0.20 (0.71), residues: 53
  sheet: -2.55 (0.32), residues: 206
  loop : -2.25 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 128 
 HIS   0.014   0.003   HIS A 292 
 PHE   0.038   0.003   PHE A 156 
 TYR   0.023   0.003   TYR A 275 
 ARG   0.010   0.001   ARG A 360 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    1)
  link_NAG-ASN         : angle       1.73512 (    3)
  hydrogen bonds       : bond        0.05612 (  143)
  hydrogen bonds       : angle       9.00805 (  405)
  SS BOND              : bond        0.01109 (    9)
  SS BOND              : angle       1.75536 (   18)
  covalent geometry    : bond        0.00879 ( 4136)
  covalent geometry    : angle       1.04879 ( 5611)

*********************** 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
  80 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8368 (tttm)
REVERT: A  163 GLN cc_start: 0.8125 (pt0) cc_final: 0.7640 (tm-30)
REVERT: A  279 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7694 (mp0)
REVERT: A  293 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7205 (mp10)
REVERT: A  343 GLU cc_start: 0.8649 (tp30) cc_final: 0.8435 (tp30)
REVERT: A  366 TYR cc_start: 0.8349 (t80) cc_final: 0.8090 (t80)
REVERT: A  464 MET cc_start: 0.7492 (tpp) cc_final: 0.7231 (tpp)
  outliers start: 16
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1737
  time to fit residues: 16.6603
Evaluate side-chains
  58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
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  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  294 THR
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 10 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.5480 r_free = 0.5480 target = 0.360300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.5383 r_free = 0.5383 target = 0.204486 restraints weight = 4409.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5345 r_free = 0.5345 target = 0.183144 restraints weight = 5673.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.172336 restraints weight = 4439.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.5049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   4146  Z= 0.327
  Angle     :  0.906   9.551   5632  Z= 0.490
  Chirality :  0.052   0.218    604
  Planarity :  0.006   0.054    738
  Dihedral  :  6.915  28.910    579
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 20.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.67 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.35), residues: 505
  helix: -0.68 (0.67), residues: 58
  sheet: -2.81 (0.31), residues: 213
  loop : -2.16 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 128 
 HIS   0.011   0.002   HIS A 285 
 PHE   0.025   0.002   PHE A 156 
 TYR   0.018   0.002   TYR A 275 
 ARG   0.006   0.001   ARG A 360 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00025 (    1)
  link_NAG-ASN         : angle       1.16190 (    3)
  hydrogen bonds       : bond        0.04190 (  143)
  hydrogen bonds       : angle       8.49246 (  405)
  SS BOND              : bond        0.01010 (    9)
  SS BOND              : angle       1.34581 (   18)
  covalent geometry    : bond        0.00593 ( 4136)
  covalent geometry    : angle       0.90445 ( 5611)

*********************** 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
  70 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7517 (mp0)
REVERT: A  343 GLU cc_start: 0.8671 (tp30) cc_final: 0.8466 (tp30)
REVERT: A  372 ARG cc_start: 0.7656 (ppt170) cc_final: 0.7202 (ppt170)
REVERT: A  464 MET cc_start: 0.7428 (tpp) cc_final: 0.6757 (tpp)
REVERT: A  477 LEU cc_start: 0.9160 (tt) cc_final: 0.8839 (mt)
REVERT: A  488 TRP cc_start: 0.5106 (p90) cc_final: 0.3580 (t60)
  outliers start: 14
  outliers final: 7
  residues processed: 66
  average time/residue: 0.1940
  time to fit residues: 15.6247
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  223 ILE
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  360 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.0030
   chunk 16 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0770
   chunk 5 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.6154

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5460 r_free = 0.5460 target = 0.357729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5333 r_free = 0.5333 target = 0.186179 restraints weight = 4445.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.181094 restraints weight = 7430.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.178781 restraints weight = 5565.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.5029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.6574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4146  Z= 0.311
  Angle     :  0.930  10.853   5632  Z= 0.497
  Chirality :  0.053   0.326    604
  Planarity :  0.006   0.049    738
  Dihedral  :  6.738  28.521    579
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.08 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.09 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.35), residues: 505
  helix: -0.52 (0.70), residues: 58
  sheet: -2.85 (0.31), residues: 213
  loop : -2.10 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 128 
 HIS   0.010   0.002   HIS A 285 
 PHE   0.025   0.003   PHE A 156 
 TYR   0.021   0.002   TYR A 162 
 ARG   0.006   0.001   ARG A 360 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00015 (    1)
  link_NAG-ASN         : angle       1.29779 (    3)
  hydrogen bonds       : bond        0.04040 (  143)
  hydrogen bonds       : angle       8.42426 (  405)
  SS BOND              : bond        0.01242 (    9)
  SS BOND              : angle       2.29460 (   18)
  covalent geometry    : bond        0.00567 ( 4136)
  covalent geometry    : angle       0.92257 ( 5611)

*********************** 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
  67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: A  343 GLU cc_start: 0.8720 (tp30) cc_final: 0.8471 (tp30)
REVERT: A  438 LEU cc_start: 0.8974 (mt) cc_final: 0.8621 (mm)
REVERT: A  464 MET cc_start: 0.7490 (tpp) cc_final: 0.6763 (tpp)
REVERT: A  477 LEU cc_start: 0.9172 (tt) cc_final: 0.8865 (mt)
REVERT: A  488 TRP cc_start: 0.5804 (p90) cc_final: 0.3582 (t60)
REVERT: A  490 ASP cc_start: 0.3441 (OUTLIER) cc_final: 0.2857 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1761
  time to fit residues: 13.4964
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  490 ASP
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 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5473 r_free = 0.5473 target = 0.363478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5392 r_free = 0.5392 target = 0.229683 restraints weight = 4466.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5384 r_free = 0.5384 target = 0.182857 restraints weight = 5030.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.178696 restraints weight = 5406.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.5061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.6731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4146  Z= 0.207
  Angle     :  0.856  15.396   5632  Z= 0.452
  Chirality :  0.049   0.185    604
  Planarity :  0.005   0.045    738
  Dihedral  :  6.074  23.996    579
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.18 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.35), residues: 505
  helix: -0.75 (0.66), residues: 58
  sheet: -2.46 (0.33), residues: 204
  loop : -2.00 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 482 
 HIS   0.005   0.001   HIS A 285 
 PHE   0.019   0.002   PHE A 156 
 TYR   0.013   0.002   TYR A 211 
 ARG   0.006   0.001   ARG A 360 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00086 (    1)
  link_NAG-ASN         : angle       1.39006 (    3)
  hydrogen bonds       : bond        0.03161 (  143)
  hydrogen bonds       : angle       7.60106 (  405)
  SS BOND              : bond        0.01065 (    9)
  SS BOND              : angle       3.41445 (   18)
  covalent geometry    : bond        0.00369 ( 4136)
  covalent geometry    : angle       0.83472 ( 5611)

*********************** 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
  67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7655 (tm-30)
REVERT: A  251 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7174 (t70)
REVERT: A  262 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6664 (mp10)
REVERT: A  293 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7345 (mp10)
REVERT: A  464 MET cc_start: 0.7408 (tpp) cc_final: 0.6659 (tpp)
REVERT: A  477 LEU cc_start: 0.9190 (tt) cc_final: 0.8881 (mt)
REVERT: A  488 TRP cc_start: 0.5852 (p90) cc_final: 0.3472 (t60)
  outliers start: 21
  outliers final: 10
  residues processed: 63
  average time/residue: 0.1799
  time to fit residues: 13.9308
Evaluate side-chains
  52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  293 GLN
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 8 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 46 optimal weight:   30.0000
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   overall best weight:    3.3386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5441 r_free = 0.5441 target = 0.356009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.187669 restraints weight = 4386.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.173129 restraints weight = 6619.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.170693 restraints weight = 5261.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.5011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.7115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4146  Z= 0.287
  Angle     :  0.950  16.374   5632  Z= 0.501
  Chirality :  0.054   0.402    604
  Planarity :  0.006   0.044    738
  Dihedral  :  6.519  24.242    579
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.68 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 19.86 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.35), residues: 505
  helix: -0.75 (0.64), residues: 58
  sheet: -2.64 (0.32), residues: 213
  loop : -2.07 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 482 
 HIS   0.009   0.002   HIS A 285 
 PHE   0.023   0.002   PHE A 518 
 TYR   0.020   0.002   TYR A 166 
 ARG   0.003   0.000   ARG A  86 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.49329 (    3)
  hydrogen bonds       : bond        0.03942 (  143)
  hydrogen bonds       : angle       8.18400 (  405)
  SS BOND              : bond        0.00922 (    9)
  SS BOND              : angle       3.46883 (   18)
  covalent geometry    : bond        0.00522 ( 4136)
  covalent geometry    : angle       0.93085 ( 5611)

*********************** 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
  63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7909 (tm-30)
REVERT: A  262 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6792 (mp10)
REVERT: A  293 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7338 (mp10)
REVERT: A  343 GLU cc_start: 0.8790 (tp30) cc_final: 0.8554 (tp30)
REVERT: A  477 LEU cc_start: 0.9189 (tt) cc_final: 0.8889 (mt)
REVERT: A  488 TRP cc_start: 0.5953 (p90) cc_final: 0.3492 (t60)
  outliers start: 19
  outliers final: 12
  residues processed: 57
  average time/residue: 0.3304
  time to fit residues: 23.4593
Evaluate side-chains
  57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 MET
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  293 GLN
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 8 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5429 r_free = 0.5429 target = 0.356489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.180711 restraints weight = 4444.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.170439 restraints weight = 6642.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.5280 r_free = 0.5280 target = 0.166350 restraints weight = 5417.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.4978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.7324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4146  Z= 0.270
  Angle     :  1.084  34.607   5632  Z= 0.553
  Chirality :  0.054   0.495    604
  Planarity :  0.006   0.054    738
  Dihedral  :  6.333  21.655    579
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.86 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.35), residues: 505
  helix: -0.61 (0.62), residues: 58
  sheet: -2.64 (0.33), residues: 213
  loop : -2.04 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 482 
 HIS   0.008   0.001   HIS A 285 
 PHE   0.024   0.002   PHE A 168 
 TYR   0.020   0.002   TYR A 166 
 ARG   0.006   0.000   ARG A 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.44831 (    3)
  hydrogen bonds       : bond        0.03943 (  143)
  hydrogen bonds       : angle       8.00789 (  405)
  SS BOND              : bond        0.01818 (    9)
  SS BOND              : angle       4.42798 (   18)
  covalent geometry    : bond        0.00479 ( 4136)
  covalent geometry    : angle       1.05585 ( 5611)

*********************** 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
  64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7854 (tm-30)
REVERT: A  129 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7237 (ptm160)
REVERT: A  251 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7055 (t70)
REVERT: A  262 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6819 (mp10)
REVERT: A  293 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7289 (mp10)
REVERT: A  343 GLU cc_start: 0.8793 (tp30) cc_final: 0.8558 (tp30)
REVERT: A  477 LEU cc_start: 0.9218 (tt) cc_final: 0.8920 (mt)
REVERT: A  488 TRP cc_start: 0.5763 (p90) cc_final: 0.3242 (t60)
  outliers start: 21
  outliers final: 12
  residues processed: 60
  average time/residue: 0.2946
  time to fit residues: 21.0140
Evaluate side-chains
  58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 MET
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  320 THR
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 44 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 7 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 299 HIS ** 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 = 0.5420 r_free = 0.5420 target = 0.354241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5281 r_free = 0.5281 target = 0.179113 restraints weight = 4398.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.170845 restraints weight = 6533.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.164420 restraints weight = 5801.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.7566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4146  Z= 0.301
  Angle     :  1.115  31.458   5632  Z= 0.566
  Chirality :  0.057   0.536    604
  Planarity :  0.006   0.043    738
  Dihedral  :  6.617  23.305    579
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 19.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 20.32 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.35), residues: 505
  helix: -0.13 (0.65), residues: 52
  sheet: -2.83 (0.31), residues: 220
  loop : -2.08 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 482 
 HIS   0.010   0.002   HIS A 285 
 PHE   0.027   0.003   PHE A 168 
 TYR   0.022   0.002   TYR A 166 
 ARG   0.007   0.001   ARG A 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    1)
  link_NAG-ASN         : angle       1.52500 (    3)
  hydrogen bonds       : bond        0.04302 (  143)
  hydrogen bonds       : angle       8.35128 (  405)
  SS BOND              : bond        0.01541 (    9)
  SS BOND              : angle       4.28988 (   18)
  covalent geometry    : bond        0.00540 ( 4136)
  covalent geometry    : angle       1.09014 ( 5611)

*********************** 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
  69 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8198 (tt0) cc_final: 0.7915 (tm-30)
REVERT: A  114 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: A  129 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7275 (ptm160)
REVERT: A  251 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7287 (t70)
REVERT: A  257 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: A  262 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6870 (mp10)
REVERT: A  276 LYS cc_start: 0.8859 (mttt) cc_final: 0.7903 (tmtt)
REVERT: A  293 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7359 (mp10)
REVERT: A  477 LEU cc_start: 0.9216 (tt) cc_final: 0.8917 (mt)
REVERT: A  488 TRP cc_start: 0.5701 (p90) cc_final: 0.3633 (t60)
  outliers start: 21
  outliers final: 11
  residues processed: 65
  average time/residue: 0.4418
  time to fit residues: 36.1243
Evaluate side-chains
  63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  123 ASN
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  320 THR
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:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0570
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.7104

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5433 r_free = 0.5433 target = 0.357682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.232432 restraints weight = 4403.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.174557 restraints weight = 4719.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5285 r_free = 0.5285 target = 0.171908 restraints weight = 5555.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.5015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.7722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4146  Z= 0.256
  Angle     :  1.076  31.432   5632  Z= 0.546
  Chirality :  0.055   0.483    604
  Planarity :  0.005   0.043    738
  Dihedral  :  6.334  21.975    579
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.78 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.36), residues: 505
  helix:  0.06 (0.67), residues: 52
  sheet: -2.63 (0.32), residues: 225
  loop : -1.99 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 482 
 HIS   0.008   0.001   HIS A 285 
 PHE   0.021   0.002   PHE A 168 
 TYR   0.021   0.002   TYR A 536 
 ARG   0.006   0.001   ARG A 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00019 (    1)
  link_NAG-ASN         : angle       1.66379 (    3)
  hydrogen bonds       : bond        0.03730 (  143)
  hydrogen bonds       : angle       7.90864 (  405)
  SS BOND              : bond        0.01580 (    9)
  SS BOND              : angle       4.33518 (   18)
  covalent geometry    : bond        0.00454 ( 4136)
  covalent geometry    : angle       1.04920 ( 5611)

*********************** 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
  63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7178 (ptm160)
REVERT: A  169 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8030 (p0)
REVERT: A  251 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7018 (t70)
REVERT: A  262 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6735 (mp10)
REVERT: A  276 LYS cc_start: 0.8621 (mttt) cc_final: 0.7651 (tmtt)
REVERT: A  283 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7893 (tptp)
REVERT: A  293 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7330 (mp10)
REVERT: A  477 LEU cc_start: 0.9213 (tt) cc_final: 0.8939 (mt)
REVERT: A  488 TRP cc_start: 0.5733 (p90) cc_final: 0.3530 (t60)
  outliers start: 18
  outliers final: 8
  residues processed: 61
  average time/residue: 0.2104
  time to fit residues: 15.4607
Evaluate side-chains
  58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  320 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5470 r_free = 0.5470 target = 0.365354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5411 r_free = 0.5411 target = 0.244284 restraints weight = 4385.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5392 r_free = 0.5392 target = 0.189109 restraints weight = 4560.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 78)----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.178691 restraints weight = 4870.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.5069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.7625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4146  Z= 0.192
  Angle     :  1.007  27.484   5632  Z= 0.500
  Chirality :  0.053   0.465    604
  Planarity :  0.005   0.042    738
  Dihedral  :  5.630  21.299    579
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.15 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.36), residues: 505
  helix: -0.03 (0.68), residues: 52
  sheet: -2.23 (0.33), residues: 216
  loop : -1.99 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 327 
 HIS   0.004   0.001   HIS A 189 
 PHE   0.025   0.002   PHE A 518 
 TYR   0.031   0.002   TYR A 536 
 ARG   0.006   0.001   ARG A 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.73222 (    3)
  hydrogen bonds       : bond        0.03493 (  143)
  hydrogen bonds       : angle       7.00016 (  405)
  SS BOND              : bond        0.01184 (    9)
  SS BOND              : angle       4.25706 (   18)
  covalent geometry    : bond        0.00351 ( 4136)
  covalent geometry    : angle       0.97863 ( 5611)

********************** 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
  56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8134 (tt0) cc_final: 0.7900 (tm-30)
REVERT: A  129 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7308 (ttt-90)
REVERT: A  169 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7646 (p0)
REVERT: A  251 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7317 (t70)
REVERT: A  262 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6634 (mp10)
REVERT: A  276 LYS cc_start: 0.8485 (mttt) cc_final: 0.7617 (tmtt)
REVERT: A  477 LEU cc_start: 0.9222 (tt) cc_final: 0.8930 (mt)
REVERT: A  488 TRP cc_start: 0.5846 (p90) cc_final: 0.3370 (t60)
  outliers start: 12
  outliers final: 7
  residues processed: 56
  average time/residue: 0.2251
  time to fit residues: 15.2509
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  172 THR
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  262 GLN
Chi-restraints excluded: chain A residue  320 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5421 r_free = 0.5421 target = 0.356883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.231679 restraints weight = 4411.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5272 r_free = 0.5272 target = 0.174556 restraints weight = 4696.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.170388 restraints weight = 5664.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.5003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.7918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4146  Z= 0.269
  Angle     :  1.065  28.581   5632  Z= 0.540
  Chirality :  0.054   0.456    604
  Planarity :  0.005   0.042    738
  Dihedral  :  6.377  22.706    579
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.60 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.36), residues: 505
  helix:  0.11 (0.69), residues: 52
  sheet: -2.68 (0.32), residues: 219
  loop : -1.92 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 482 
 HIS   0.009   0.001   HIS A 285 
 PHE   0.024   0.002   PHE A 168 
 TYR   0.027   0.002   TYR A 536 
 ARG   0.008   0.001   ARG A  70 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       1.66939 (    3)
  hydrogen bonds       : bond        0.03927 (  143)
  hydrogen bonds       : angle       7.85416 (  405)
  SS BOND              : bond        0.01478 (    9)
  SS BOND              : angle       4.29131 (   18)
  covalent geometry    : bond        0.00491 ( 4136)
  covalent geometry    : angle       1.03870 ( 5611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2131.83 seconds
wall clock time: 39 minutes 37.99 seconds (2377.99 seconds total)