Starting phenix.real_space_refine
on Mon Jul 28 21:49:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q49_13799/07_2025/7q49_13799_trim.cif"
  }
  resolution = 3.72
  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=   0.003 sd=   0.059
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      19      5.16       5
     C    3398      2.51       5
     N     873      2.21       5
     O    1045      1.98       5
     H    4788      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10124
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 9804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 9804
          Classifications: {'peptide': 616}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 577}
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 32
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.76, per 1000 atoms: 0.57
  Number of scatterers: 10124
  At special positions: 0
  Unit cell: (77.38, 89.04, 93.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      19     16.00
     O    1045      8.00
     N     873      7.00
     C    3398      6.00
     H    4788      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 330 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 528 " 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
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   5 "
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1302 " - " ASN A  82 "
      " NAG A1303 " - " ASN A 416 "
      " NAG B   1 " - " ASN A  25 "
      " NAG C   1 " - " ASN A 289 "
      " NAG D   1 " - " ASN A   9 "
      " NAG E   1 " - " ASN A 117 "
      " NAG F   1 " - " ASN A  45 "
      " NAG G   1 " - " ASN A 480 "
  Time building additional restraints: 3.88
  Conformation dependent library (CDL) restraints added in 717.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1301 "
        pdb="ZN    ZN A1301 " - pdb=" NE2 HIS A 365 "
        pdb="ZN    ZN A1301 " - pdb=" NE2 HIS A 361 "


  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      70.3% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 45
      removed outlier: 3.804A  pdb=" N   GLN A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 77
      removed outlier: 3.758A  pdb=" N   GLU A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 85 through 97
    Processing helix  chain 'A' and resid 98 through 103
      removed outlier: 3.583A  pdb=" N   ALA A 101 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 125
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 152 through 190
      Proline residue:  A 170  - end of helix
      Proline residue:  A 173  - end of helix
      removed outlier: 3.644A  pdb=" N   GLU A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 188 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 201
      removed outlier: 3.803A  pdb=" N   TRP A 201 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 238
      Proline residue:  A 220  - end of helix
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 261 through 263
      No H-bonds generated for 'chain 'A' and resid 261 through 263'
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 279 through 286
      removed outlier: 3.578A  pdb=" N   GLN A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.620A  pdb=" N   ARG A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
      removed outlier: 3.966A  pdb=" N   TRP A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 373
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 386 through 401
      removed outlier: 3.590A  pdb=" N   GLY A 392 " --> pdb=" O   HIS A 388 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 417 through 433
    Processing helix  chain 'A' and resid 434 through 452
      removed outlier: 4.473A  pdb=" N   PHE A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 472
      removed outlier: 3.557A  pdb=" N   TRP A 463 " --> pdb=" O   TYR A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.682A  pdb=" N   PHE A 502 " --> pdb=" O   TYR A 498 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 509 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
    Processing helix  chain 'A' and resid 533 through 547
      removed outlier: 3.526A  pdb=" N   LYS A 539 " --> pdb=" O   LYS A 535 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 567 through 574
    Processing helix  chain 'A' and resid 574 through 589
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127
    Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249
      removed outlier: 6.065A  pdb=" N   ILE A 248 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 336

    294 hydrogen bonds defined for protein.
    843 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: 4.48

  Time building geometry restraints manager: 4.19 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 4787
        1.04 -     1.24: 587
        1.24 -     1.44: 1914
        1.44 -     1.63: 2960
        1.63 -     1.83: 31
  Bond restraints: 10279
  Sorted by residual:
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.358  0.048 2.00e-02 2.50e+03 5.71e+00
  bond pdb=" C5  BMA F   3 "
       pdb=" O5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.463 -0.046 2.00e-02 2.50e+03 5.28e+00
  bond pdb=" C1  MAN B   4 "
       pdb=" C2  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.568 -0.042 2.00e-02 2.50e+03 4.44e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" C2  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.532  1.491  0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.366  0.040 2.00e-02 2.50e+03 3.95e+00
  ... (remaining 10274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17208
        1.59 -     3.17: 956
        3.17 -     4.76: 158
        4.76 -     6.35: 29
        6.35 -     7.93: 9
  Bond angle restraints: 18360
  Sorted by residual:
  angle pdb=" C   LYS A 341 "
        pdb=" N   ASP A 342 "
        pdb=" CA  ASP A 342 "
      ideal   model   delta    sigma   weight residual
     121.62  115.31    6.31 1.83e+00 2.99e-01 1.19e+01
  angle pdb=" N   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" C   LYS A 321 "
      ideal   model   delta    sigma   weight residual
     109.81  102.50    7.31 2.21e+00 2.05e-01 1.09e+01
  angle pdb=" CA  TYR A 338 "
        pdb=" CB  TYR A 338 "
        pdb=" CG  TYR A 338 "
      ideal   model   delta    sigma   weight residual
     113.90  108.25    5.65 1.80e+00 3.09e-01 9.85e+00
  angle pdb=" N   THR A 349 "
        pdb=" CA  THR A 349 "
        pdb=" C   THR A 349 "
      ideal   model   delta    sigma   weight residual
     110.23  114.52   -4.29 1.45e+00 4.76e-01 8.77e+00
  angle pdb=" N   PHE A  83 "
        pdb=" CA  PHE A  83 "
        pdb=" CB  PHE A  83 "
      ideal   model   delta    sigma   weight residual
     109.48  113.98   -4.50 1.55e+00 4.16e-01 8.42e+00
  ... (remaining 18355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.35: 4789
       21.35 -    42.69: 288
       42.69 -    64.04: 98
       64.04 -    85.39: 49
       85.39 -   106.73: 29
  Dihedral angle restraints: 5253
    sinusoidal: 2996
      harmonic: 2257
  Sorted by residual:
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.02  106.73     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C3  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -57.53  105.15     1      3.00e+01 1.11e-03 1.35e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -175.74  104.45     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 5250 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 682
       0.066 -    0.132: 146
       0.132 -    0.198: 14
       0.198 -    0.264: 5
       0.264 -    0.330: 7
  Chirality restraints: 854
  Sorted by residual:
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.60    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.59    0.32 2.00e-01 2.50e+01 2.51e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.58    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 851 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 508 "   -0.046 2.00e-02 2.50e+03   5.32e-02 4.25e+01
        pdb=" CD  GLN A 508 "    0.050 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 508 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 508 "    0.077 2.00e-02 2.50e+03
        pdb="HE21 GLN A 508 "    0.003 2.00e-02 2.50e+03
        pdb="HE22 GLN A 508 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 479 "   -0.130 9.50e-02 1.11e+02   5.15e-02 1.91e+01
        pdb=" NE  ARG A 479 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 479 "   -0.039 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 479 "   -0.039 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 479 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG A 479 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 479 "    0.045 2.00e-02 2.50e+03
        pdb="HH21 ARG A 479 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 479 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 371 "    0.028 2.00e-02 2.50e+03   3.34e-02 1.67e+01
        pdb=" CD  GLN A 371 "   -0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 371 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 371 "   -0.051 2.00e-02 2.50e+03
        pdb="HE21 GLN A 371 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A 371 "    0.050 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 309
        2.14 -     2.76: 18476
        2.76 -     3.37: 28899
        3.37 -     3.99: 35865
        3.99 -     4.60: 56711
  Nonbonded interactions: 140260
  Sorted by model distance:
  nonbonded pdb=" HG1 THR A 454 "
            pdb=" OD2 ASP A 462 "
     model   vdw
     1.526 2.450
  nonbonded pdb=" HG1 THR A 468 "
            pdb=" O   ILE A 473 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HH  TYR A 521 "
            pdb=" O   PRO A 524 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" O   TRP A  40 "
            pdb=" HG1 THR A  44 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD2 ASP A 443 "
            pdb=" H   ILE A 499 "
     model   vdw
     1.594 2.450
  ... (remaining 140255 not shown)

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

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:             4.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.150
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     32.440
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
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      :  0.008   0.048   5521  Z= 0.383
  Angle     :  1.149  12.193   7565  Z= 0.582
  Chirality :  0.061   0.330    854
  Planarity :  0.009   0.105    935
  Dihedral  : 19.174 106.734   2370
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.70 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.50 (0.30), residues: 614
  helix: -0.60 (0.22), residues: 367
  sheet: -0.97 (1.76), residues: 10
  loop : -1.48 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.006   TRP A 257 
 HIS   0.010   0.003   HIS A 331 
 PHE   0.028   0.004   PHE A 509 
 TYR   0.032   0.005   TYR A 338 
 ARG   0.031   0.005   ARG A 479 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00977 (    8)
  link_NAG-ASN         : angle       5.50364 (   24)
  link_ALPHA1-6        : bond        0.00820 (    2)
  link_ALPHA1-6        : angle       1.40444 (    6)
  link_BETA1-4         : bond        0.00557 (   12)
  link_BETA1-4         : angle       3.37957 (   36)
  link_ALPHA1-3        : bond        0.00376 (    2)
  link_ALPHA1-3        : angle       3.15416 (    6)
  hydrogen bonds       : bond        0.24029 (  294)
  hydrogen bonds       : angle       8.35387 (  843)
  link_BETA1-6         : bond        0.00342 (    1)
  link_BETA1-6         : angle       1.24911 (    3)
  metal coordination   : bond        0.00936 (    2)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       2.13321 (    6)
  covalent geometry    : bond        0.00829 ( 5491)
  covalent geometry    : angle       1.08126 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLU cc_start: 0.8231 (pt0) cc_final: 0.8019 (tt0)
REVERT: A   52 ARG cc_start: 0.8909 (tpt170) cc_final: 0.8677 (ttp-110)
REVERT: A   64 PHE cc_start: 0.7995 (t80) cc_final: 0.7661 (t80)
REVERT: A  132 LYS cc_start: 0.8260 (tttt) cc_final: 0.7988 (mmmt)
REVERT: A  155 MET cc_start: 0.8060 (tpt) cc_final: 0.7768 (tpt)
REVERT: A  156 LEU cc_start: 0.9086 (tp) cc_final: 0.8769 (tp)
REVERT: A  182 SER cc_start: 0.9198 (t) cc_final: 0.8765 (m)
REVERT: A  183 ASN cc_start: 0.8341 (m-40) cc_final: 0.8080 (t0)
REVERT: A  298 GLU cc_start: 0.8454 (tt0) cc_final: 0.7972 (tm-30)
REVERT: A  302 THR cc_start: 0.9124 (p) cc_final: 0.8425 (p)
REVERT: A  341 LYS cc_start: 0.7998 (mttt) cc_final: 0.7673 (mmpt)
REVERT: A  350 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7386 (ttm170)
REVERT: A  453 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6909 (tmm160)
REVERT: A  579 GLN cc_start: 0.7818 (tt0) cc_final: 0.7450 (tm-30)
REVERT: A  592 LEU cc_start: 0.8423 (mt) cc_final: 0.8166 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.4882
  time to fit residues: 75.4101
Evaluate side-chains
  81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
A 292 HIS
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 GLN
A 575 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.114829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.095583 restraints weight = 27056.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.100528 restraints weight = 10444.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.103623 restraints weight = 5347.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5521  Z= 0.185
  Angle     :  0.826   9.868   7565  Z= 0.421
  Chirality :  0.044   0.233    854
  Planarity :  0.006   0.046    935
  Dihedral  : 14.481  72.619   1180
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.87 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.32), residues: 614
  helix:  0.57 (0.25), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.73 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 552 
 HIS   0.011   0.002   HIS A 360 
 PHE   0.030   0.002   PHE A 294 
 TYR   0.017   0.002   TYR A 215 
 ARG   0.003   0.001   ARG A 151 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    8)
  link_NAG-ASN         : angle       2.59925 (   24)
  link_ALPHA1-6        : bond        0.00313 (    2)
  link_ALPHA1-6        : angle       1.62577 (    6)
  link_BETA1-4         : bond        0.00539 (   12)
  link_BETA1-4         : angle       2.40211 (   36)
  link_ALPHA1-3        : bond        0.00370 (    2)
  link_ALPHA1-3        : angle       2.21532 (    6)
  hydrogen bonds       : bond        0.08336 (  294)
  hydrogen bonds       : angle       5.75153 (  843)
  link_BETA1-6         : bond        0.00142 (    1)
  link_BETA1-6         : angle       1.39541 (    3)
  metal coordination   : bond        0.00242 (    2)
  SS BOND              : bond        0.00190 (    3)
  SS BOND              : angle       2.61901 (    6)
  covalent geometry    : bond        0.00376 ( 5491)
  covalent geometry    : angle       0.79192 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8651 (ttp-110)
REVERT: A  132 LYS cc_start: 0.8184 (tttt) cc_final: 0.7915 (mmmt)
REVERT: A  161 GLU cc_start: 0.8321 (tt0) cc_final: 0.7971 (tt0)
REVERT: A  182 SER cc_start: 0.9103 (t) cc_final: 0.8693 (m)
REVERT: A  183 ASN cc_start: 0.8297 (m-40) cc_final: 0.7952 (t0)
REVERT: A  350 ARG cc_start: 0.7473 (ttt180) cc_final: 0.7249 (ttm170)
REVERT: A  379 LEU cc_start: 0.8087 (mt) cc_final: 0.7749 (mt)
REVERT: A  453 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6870 (tmm160)
REVERT: A  462 ASP cc_start: 0.8049 (m-30) cc_final: 0.7189 (t0)
REVERT: A  582 GLN cc_start: 0.7865 (mt0) cc_final: 0.7382 (tp40)
  outliers start: 6
  outliers final: 5
  residues processed: 101
  average time/residue: 0.4097
  time to fit residues: 52.2145
Evaluate side-chains
  88 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 360 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 = 0.3632 r_free = 0.3632 target = 0.115530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.094996 restraints weight = 28244.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.099742 restraints weight = 11150.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.102799 restraints weight = 5888.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5521  Z= 0.166
  Angle     :  0.719   6.137   7565  Z= 0.358
  Chirality :  0.041   0.189    854
  Planarity :  0.005   0.054    935
  Dihedral  : 10.380  61.339   1180
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.32 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.33), residues: 614
  helix:  0.92 (0.25), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.22 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.012   0.002   HIS A 251 
 PHE   0.017   0.002   PHE A 294 
 TYR   0.017   0.002   TYR A 368 
 ARG   0.003   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00254 (    8)
  link_NAG-ASN         : angle       1.85649 (   24)
  link_ALPHA1-6        : bond        0.00403 (    2)
  link_ALPHA1-6        : angle       1.62545 (    6)
  link_BETA1-4         : bond        0.00361 (   12)
  link_BETA1-4         : angle       2.35493 (   36)
  link_ALPHA1-3        : bond        0.00977 (    2)
  link_ALPHA1-3        : angle       2.11173 (    6)
  hydrogen bonds       : bond        0.06407 (  294)
  hydrogen bonds       : angle       5.27660 (  843)
  link_BETA1-6         : bond        0.00340 (    1)
  link_BETA1-6         : angle       1.29664 (    3)
  metal coordination   : bond        0.00116 (    2)
  SS BOND              : bond        0.00618 (    3)
  SS BOND              : angle       1.23019 (    6)
  covalent geometry    : bond        0.00352 ( 5491)
  covalent geometry    : angle       0.69044 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6523 (tt)
REVERT: A  182 SER cc_start: 0.9115 (t) cc_final: 0.8884 (m)
REVERT: A  183 ASN cc_start: 0.8408 (m-40) cc_final: 0.7719 (t0)
REVERT: A  215 TYR cc_start: 0.7151 (t80) cc_final: 0.6820 (t80)
REVERT: A  309 MET cc_start: 0.9016 (mmp) cc_final: 0.8796 (mmp)
REVERT: A  338 TYR cc_start: 0.9228 (m-80) cc_final: 0.8987 (m-10)
REVERT: A  350 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7455 (ttm170)
REVERT: A  453 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7111 (tmm160)
REVERT: A  462 ASP cc_start: 0.8164 (m-30) cc_final: 0.7485 (t70)
REVERT: A  582 GLN cc_start: 0.8125 (mt0) cc_final: 0.7661 (tp40)
  outliers start: 7
  outliers final: 5
  residues processed: 93
  average time/residue: 0.5652
  time to fit residues: 66.4668
Evaluate side-chains
  82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.115477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095033 restraints weight = 28247.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.099723 restraints weight = 11145.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.102755 restraints weight = 5899.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5521  Z= 0.157
  Angle     :  0.657   5.749   7565  Z= 0.328
  Chirality :  0.039   0.180    854
  Planarity :  0.004   0.056    935
  Dihedral  :  8.564  59.893   1180
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.08 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.34), residues: 614
  helix:  1.04 (0.26), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.10 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 552 
 HIS   0.009   0.001   HIS A 251 
 PHE   0.013   0.002   PHE A 509 
 TYR   0.015   0.002   TYR A 215 
 ARG   0.004   0.000   ARG A 380 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    8)
  link_NAG-ASN         : angle       1.65750 (   24)
  link_ALPHA1-6        : bond        0.00498 (    2)
  link_ALPHA1-6        : angle       1.58100 (    6)
  link_BETA1-4         : bond        0.00304 (   12)
  link_BETA1-4         : angle       2.17032 (   36)
  link_ALPHA1-3        : bond        0.00999 (    2)
  link_ALPHA1-3        : angle       2.21741 (    6)
  hydrogen bonds       : bond        0.05828 (  294)
  hydrogen bonds       : angle       5.03970 (  843)
  link_BETA1-6         : bond        0.00406 (    1)
  link_BETA1-6         : angle       1.29149 (    3)
  metal coordination   : bond        0.00156 (    2)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       0.89570 (    6)
  covalent geometry    : bond        0.00334 ( 5491)
  covalent geometry    : angle       0.63049 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 LEU cc_start: 0.9108 (tp) cc_final: 0.8817 (tp)
REVERT: A  182 SER cc_start: 0.9129 (t) cc_final: 0.8891 (m)
REVERT: A  183 ASN cc_start: 0.8442 (m-40) cc_final: 0.8202 (t0)
REVERT: A  215 TYR cc_start: 0.7175 (t80) cc_final: 0.6868 (t80)
REVERT: A  338 TYR cc_start: 0.9192 (m-80) cc_final: 0.8913 (m-10)
REVERT: A  350 ARG cc_start: 0.7707 (ttt180) cc_final: 0.7402 (ttm170)
REVERT: A  453 ARG cc_start: 0.7442 (mtt90) cc_final: 0.7085 (tmm160)
REVERT: A  462 ASP cc_start: 0.8143 (m-30) cc_final: 0.7445 (t0)
REVERT: A  582 GLN cc_start: 0.8181 (mt0) cc_final: 0.7715 (tp40)
  outliers start: 13
  outliers final: 8
  residues processed: 93
  average time/residue: 0.4902
  time to fit residues: 58.8450
Evaluate side-chains
  80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.113499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.093572 restraints weight = 28794.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.098078 restraints weight = 11410.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.100973 restraints weight = 6069.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5521  Z= 0.217
  Angle     :  0.681   5.940   7565  Z= 0.346
  Chirality :  0.040   0.188    854
  Planarity :  0.005   0.051    935
  Dihedral  :  7.978  59.069   1180
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.83 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.34), residues: 614
  helix:  0.86 (0.26), residues: 379
  sheet:  None (None), residues: 0
  loop : -0.25 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 552 
 HIS   0.009   0.002   HIS A 251 
 PHE   0.016   0.002   PHE A 509 
 TYR   0.018   0.002   TYR A 215 
 ARG   0.004   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00527 (    8)
  link_NAG-ASN         : angle       1.80256 (   24)
  link_ALPHA1-6        : bond        0.00640 (    2)
  link_ALPHA1-6        : angle       1.58551 (    6)
  link_BETA1-4         : bond        0.00441 (   12)
  link_BETA1-4         : angle       2.02177 (   36)
  link_ALPHA1-3        : bond        0.01014 (    2)
  link_ALPHA1-3        : angle       2.20936 (    6)
  hydrogen bonds       : bond        0.05601 (  294)
  hydrogen bonds       : angle       5.03965 (  843)
  link_BETA1-6         : bond        0.00421 (    1)
  link_BETA1-6         : angle       1.39446 (    3)
  metal coordination   : bond        0.00167 (    2)
  SS BOND              : bond        0.00432 (    3)
  SS BOND              : angle       1.23705 (    6)
  covalent geometry    : bond        0.00471 ( 5491)
  covalent geometry    : angle       0.65614 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8356 (t70) cc_final: 0.8136 (m-30)
REVERT: A  182 SER cc_start: 0.9143 (t) cc_final: 0.8871 (m)
REVERT: A  183 ASN cc_start: 0.8480 (m-40) cc_final: 0.8221 (t0)
REVERT: A  215 TYR cc_start: 0.7344 (t80) cc_final: 0.7073 (t80)
REVERT: A  341 LYS cc_start: 0.7898 (mttt) cc_final: 0.7541 (mmmt)
REVERT: A  350 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7455 (ttm170)
REVERT: A  453 ARG cc_start: 0.7447 (mtt90) cc_final: 0.7001 (tmm160)
REVERT: A  462 ASP cc_start: 0.8197 (m-30) cc_final: 0.7420 (t0)
REVERT: A  582 GLN cc_start: 0.8224 (mt0) cc_final: 0.7737 (tp40)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.3734
  time to fit residues: 40.5983
Evaluate side-chains
  80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0170
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.115703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.095483 restraints weight = 28456.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.100119 restraints weight = 11194.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.103100 restraints weight = 5935.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5521  Z= 0.135
  Angle     :  0.609   5.503   7565  Z= 0.305
  Chirality :  0.038   0.197    854
  Planarity :  0.004   0.048    935
  Dihedral  :  7.355  58.678   1180
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.96 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.34), residues: 614
  helix:  1.08 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.18 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 552 
 HIS   0.010   0.001   HIS A 251 
 PHE   0.010   0.001   PHE A 178 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    8)
  link_NAG-ASN         : angle       1.44601 (   24)
  link_ALPHA1-6        : bond        0.00650 (    2)
  link_ALPHA1-6        : angle       1.47552 (    6)
  link_BETA1-4         : bond        0.00268 (   12)
  link_BETA1-4         : angle       1.78750 (   36)
  link_ALPHA1-3        : bond        0.01074 (    2)
  link_ALPHA1-3        : angle       2.09371 (    6)
  hydrogen bonds       : bond        0.05269 (  294)
  hydrogen bonds       : angle       4.79126 (  843)
  link_BETA1-6         : bond        0.00525 (    1)
  link_BETA1-6         : angle       1.21234 (    3)
  metal coordination   : bond        0.00128 (    2)
  SS BOND              : bond        0.00447 (    3)
  SS BOND              : angle       0.94252 (    6)
  covalent geometry    : bond        0.00284 ( 5491)
  covalent geometry    : angle       0.58879 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 LEU cc_start: 0.9076 (tp) cc_final: 0.8775 (tp)
REVERT: A  182 SER cc_start: 0.9122 (t) cc_final: 0.8867 (m)
REVERT: A  183 ASN cc_start: 0.8450 (m-40) cc_final: 0.8207 (t0)
REVERT: A  215 TYR cc_start: 0.7091 (t80) cc_final: 0.6827 (t80)
REVERT: A  341 LYS cc_start: 0.7855 (mttt) cc_final: 0.7509 (mmmt)
REVERT: A  350 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7388 (ttm170)
REVERT: A  453 ARG cc_start: 0.7304 (mtt90) cc_final: 0.6793 (tmm160)
REVERT: A  462 ASP cc_start: 0.8190 (m-30) cc_final: 0.7989 (t70)
REVERT: A  582 GLN cc_start: 0.8230 (mt0) cc_final: 0.7889 (mm110)
  outliers start: 11
  outliers final: 11
  residues processed: 82
  average time/residue: 0.3505
  time to fit residues: 37.6050
Evaluate side-chains
  81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 42 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.115624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.095411 restraints weight = 28808.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.100001 restraints weight = 11351.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.103029 restraints weight = 6016.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5521  Z= 0.150
  Angle     :  0.604   5.552   7565  Z= 0.305
  Chirality :  0.037   0.185    854
  Planarity :  0.004   0.048    935
  Dihedral  :  7.021  58.396   1180
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.15 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.35), residues: 614
  helix:  1.17 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.25 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.009   0.001   HIS A 251 
 PHE   0.023   0.001   PHE A 511 
 TYR   0.014   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    8)
  link_NAG-ASN         : angle       1.49805 (   24)
  link_ALPHA1-6        : bond        0.00639 (    2)
  link_ALPHA1-6        : angle       1.46393 (    6)
  link_BETA1-4         : bond        0.00325 (   12)
  link_BETA1-4         : angle       1.75620 (   36)
  link_ALPHA1-3        : bond        0.00997 (    2)
  link_ALPHA1-3        : angle       2.01767 (    6)
  hydrogen bonds       : bond        0.05079 (  294)
  hydrogen bonds       : angle       4.73698 (  843)
  link_BETA1-6         : bond        0.00477 (    1)
  link_BETA1-6         : angle       1.29528 (    3)
  metal coordination   : bond        0.00153 (    2)
  SS BOND              : bond        0.00354 (    3)
  SS BOND              : angle       0.75792 (    6)
  covalent geometry    : bond        0.00320 ( 5491)
  covalent geometry    : angle       0.58373 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 SER cc_start: 0.9115 (t) cc_final: 0.8860 (m)
REVERT: A  183 ASN cc_start: 0.8447 (m-40) cc_final: 0.8187 (t0)
REVERT: A  215 TYR cc_start: 0.7143 (t80) cc_final: 0.6863 (t80)
REVERT: A  341 LYS cc_start: 0.7872 (mttt) cc_final: 0.7513 (mmmt)
REVERT: A  453 ARG cc_start: 0.7323 (mtt90) cc_final: 0.6800 (tmm160)
REVERT: A  462 ASP cc_start: 0.8158 (m-30) cc_final: 0.7933 (t70)
REVERT: A  529 ASP cc_start: 0.8554 (p0) cc_final: 0.8323 (p0)
REVERT: A  582 GLN cc_start: 0.8241 (mt0) cc_final: 0.7906 (mm110)
  outliers start: 12
  outliers final: 10
  residues processed: 77
  average time/residue: 0.4338
  time to fit residues: 44.1965
Evaluate side-chains
  79 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0670
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1520

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.112037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.091555 restraints weight = 29214.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096510 restraints weight = 10980.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099708 restraints weight = 5674.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5521  Z= 0.165
  Angle     :  0.608   6.414   7565  Z= 0.309
  Chirality :  0.037   0.187    854
  Planarity :  0.004   0.047    935
  Dihedral  :  6.831  57.889   1180
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.72 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.35), residues: 614
  helix:  1.16 (0.27), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.29 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.008   0.001   HIS A 251 
 PHE   0.017   0.001   PHE A 511 
 TYR   0.015   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    8)
  link_NAG-ASN         : angle       1.47515 (   24)
  link_ALPHA1-6        : bond        0.00658 (    2)
  link_ALPHA1-6        : angle       1.43162 (    6)
  link_BETA1-4         : bond        0.00347 (   12)
  link_BETA1-4         : angle       1.72129 (   36)
  link_ALPHA1-3        : bond        0.00978 (    2)
  link_ALPHA1-3        : angle       1.98733 (    6)
  hydrogen bonds       : bond        0.04992 (  294)
  hydrogen bonds       : angle       4.74110 (  843)
  link_BETA1-6         : bond        0.00483 (    1)
  link_BETA1-6         : angle       1.30586 (    3)
  metal coordination   : bond        0.00162 (    2)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       0.76764 (    6)
  covalent geometry    : bond        0.00356 ( 5491)
  covalent geometry    : angle       0.58867 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 SER cc_start: 0.9091 (t) cc_final: 0.8746 (m)
REVERT: A  183 ASN cc_start: 0.8465 (m-40) cc_final: 0.8232 (t0)
REVERT: A  341 LYS cc_start: 0.8054 (mttt) cc_final: 0.7650 (mmmt)
REVERT: A  350 ARG cc_start: 0.7812 (ttm170) cc_final: 0.6959 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6563 (tmm160)
REVERT: A  462 ASP cc_start: 0.8121 (m-30) cc_final: 0.7920 (t0)
REVERT: A  582 GLN cc_start: 0.8001 (mt0) cc_final: 0.7659 (mm110)
REVERT: A  599 TRP cc_start: 0.8221 (t60) cc_final: 0.7547 (t60)
  outliers start: 11
  outliers final: 11
  residues processed: 76
  average time/residue: 0.3965
  time to fit residues: 39.0682
Evaluate side-chains
  81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  549 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.093108 restraints weight = 28863.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098144 restraints weight = 10982.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101407 restraints weight = 5707.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5521  Z= 0.130
  Angle     :  0.570   5.326   7565  Z= 0.289
  Chirality :  0.036   0.200    854
  Planarity :  0.004   0.045    935
  Dihedral  :  6.467  57.772   1180
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.47 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.07 (0.35), residues: 614
  helix:  1.32 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.20 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.009   0.001   HIS A 251 
 PHE   0.015   0.001   PHE A 511 
 TYR   0.013   0.001   TYR A 215 
 ARG   0.002   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    8)
  link_NAG-ASN         : angle       1.31035 (   24)
  link_ALPHA1-6        : bond        0.00657 (    2)
  link_ALPHA1-6        : angle       1.38495 (    6)
  link_BETA1-4         : bond        0.00265 (   12)
  link_BETA1-4         : angle       1.59551 (   36)
  link_ALPHA1-3        : bond        0.00971 (    2)
  link_ALPHA1-3        : angle       1.87210 (    6)
  hydrogen bonds       : bond        0.04717 (  294)
  hydrogen bonds       : angle       4.60341 (  843)
  link_BETA1-6         : bond        0.00507 (    1)
  link_BETA1-6         : angle       1.26148 (    3)
  metal coordination   : bond        0.00128 (    2)
  SS BOND              : bond        0.00280 (    3)
  SS BOND              : angle       0.64442 (    6)
  covalent geometry    : bond        0.00277 ( 5491)
  covalent geometry    : angle       0.55298 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.7922 (tt0) cc_final: 0.7636 (tp40)
REVERT: A  156 LEU cc_start: 0.8884 (tp) cc_final: 0.8582 (tp)
REVERT: A  182 SER cc_start: 0.9078 (t) cc_final: 0.8719 (m)
REVERT: A  183 ASN cc_start: 0.8459 (m-40) cc_final: 0.8225 (t0)
REVERT: A  341 LYS cc_start: 0.8025 (mttt) cc_final: 0.7714 (mmpt)
REVERT: A  350 ARG cc_start: 0.7736 (ttm170) cc_final: 0.6839 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6531 (tmm160)
REVERT: A  582 GLN cc_start: 0.7909 (mt0) cc_final: 0.7575 (mm110)
REVERT: A  599 TRP cc_start: 0.8204 (t60) cc_final: 0.7526 (t60)
  outliers start: 7
  outliers final: 7
  residues processed: 74
  average time/residue: 0.3997
  time to fit residues: 39.0115
Evaluate side-chains
  75 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.093656 restraints weight = 28758.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098761 restraints weight = 10971.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.102108 restraints weight = 5710.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5521  Z= 0.122
  Angle     :  0.564   6.384   7565  Z= 0.285
  Chirality :  0.036   0.199    854
  Planarity :  0.004   0.043    935
  Dihedral  :  6.215  57.449   1180
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.09 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.22 (0.36), residues: 614
  helix:  1.44 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.17 (0.45), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 552 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.017   0.001   PHE A 511 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.002   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    8)
  link_NAG-ASN         : angle       1.31257 (   24)
  link_ALPHA1-6        : bond        0.00646 (    2)
  link_ALPHA1-6        : angle       1.38869 (    6)
  link_BETA1-4         : bond        0.00278 (   12)
  link_BETA1-4         : angle       1.55820 (   36)
  link_ALPHA1-3        : bond        0.00921 (    2)
  link_ALPHA1-3        : angle       1.79802 (    6)
  hydrogen bonds       : bond        0.04619 (  294)
  hydrogen bonds       : angle       4.54405 (  843)
  link_BETA1-6         : bond        0.00495 (    1)
  link_BETA1-6         : angle       1.25185 (    3)
  metal coordination   : bond        0.00101 (    2)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       0.60648 (    6)
  covalent geometry    : bond        0.00258 ( 5491)
  covalent geometry    : angle       0.54756 ( 7484)

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.7904 (tt0) cc_final: 0.7624 (tp40)
REVERT: A  182 SER cc_start: 0.9068 (t) cc_final: 0.8714 (m)
REVERT: A  183 ASN cc_start: 0.8490 (m-40) cc_final: 0.8264 (t0)
REVERT: A  341 LYS cc_start: 0.8005 (mttt) cc_final: 0.7695 (mmpt)
REVERT: A  350 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6803 (mtm-85)
REVERT: A  453 ARG cc_start: 0.7308 (mtt90) cc_final: 0.6477 (tmm160)
REVERT: A  582 GLN cc_start: 0.7912 (mt0) cc_final: 0.7589 (mm110)
REVERT: A  599 TRP cc_start: 0.8168 (t60) cc_final: 0.7487 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 73
  average time/residue: 0.3806
  time to fit residues: 35.8656
Evaluate side-chains
  73 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 TYR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  544 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.114772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.093845 restraints weight = 28886.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.098963 restraints weight = 10979.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.102337 restraints weight = 5699.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5521  Z= 0.125
  Angle     :  0.566   6.252   7565  Z= 0.285
  Chirality :  0.036   0.199    854
  Planarity :  0.004   0.044    935
  Dihedral  :  6.112  57.296   1180
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.91 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  1.25 (0.35), residues: 614
  helix:  1.47 (0.27), residues: 381
  sheet:  None (None), residues: 0
  loop : -0.15 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 552 
 HIS   0.009   0.001   HIS A 251 
 PHE   0.017   0.001   PHE A 511 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    8)
  link_NAG-ASN         : angle       1.26641 (   24)
  link_ALPHA1-6        : bond        0.00631 (    2)
  link_ALPHA1-6        : angle       1.38770 (    6)
  link_BETA1-4         : bond        0.00273 (   12)
  link_BETA1-4         : angle       1.55063 (   36)
  link_ALPHA1-3        : bond        0.00854 (    2)
  link_ALPHA1-3        : angle       1.73175 (    6)
  hydrogen bonds       : bond        0.04533 (  294)
  hydrogen bonds       : angle       4.50493 (  843)
  link_BETA1-6         : bond        0.00499 (    1)
  link_BETA1-6         : angle       1.26895 (    3)
  metal coordination   : bond        0.00107 (    2)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       0.61628 (    6)
  covalent geometry    : bond        0.00267 ( 5491)
  covalent geometry    : angle       0.54973 ( 7484)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4614.42 seconds
wall clock time: 81 minutes 51.53 seconds (4911.53 seconds total)