Starting phenix.real_space_refine
on Tue Jul 29 07:19:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2025/8ijx_35502.cif"
  }
  resolution = 2.08
  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=  -0.002 sd=   0.091
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: 9
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      65      5.16       5
     Cl      1      4.86       5
     Be      1      3.05       5
     C    6573      2.51       5
     N    1654      2.21       5
     O    2241      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10545
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 983, 7633
          Classifications: {'peptide': 983}
          Link IDs: {'PTRANS': 47, 'TRANS': 935}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2142
          Classifications: {'peptide': 268}
          Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 273
          Unusual residues: {' MG': 1, 'PCW': 5, 'PZ0': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'PCW:plan-4': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 124
          Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          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: 259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 259
          Classifications: {'water': 259}
          Link IDs: {None: 258}
    Chain: "B"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 114
          Classifications: {'water': 114}
          Link IDs: {None: 113}
  Time building chain proxies: 7.65, per 1000 atoms: 0.73
  Number of scatterers: 10545
  At special positions: 0
  Unit cell: (82.72, 94, 174.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     P       6     15.00
     Mg      1     11.99
     F       3      9.00
     O    2241      8.00
     N    1654      7.00
     C    6573      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 152 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 262 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 302 " - " ASN B  99 "
      " NAG B 303 " - " ASN B 130 "
      " NAG B 304 " - " ASN B 161 "
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      50.6% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 84
    Processing helix  chain 'A' and resid 96 through 105
      removed outlier: 3.526A  pdb=" N   GLN A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 131
    Processing helix  chain 'A' and resid 135 through 169
      removed outlier: 3.952A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.932A  pdb=" N   THR A 248 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 285
    Processing helix  chain 'A' and resid 291 through 322
    Processing helix  chain 'A' and resid 325 through 340
    Processing helix  chain 'A' and resid 344 through 363
      removed outlier: 3.711A  pdb=" N   LYS A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.523A  pdb=" N   ARG A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 519 through 525
    Processing helix  chain 'A' and resid 542 through 557
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 676 through 681
      removed outlier: 3.549A  pdb=" N   ASP A 681 " --> pdb=" O   MET A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 694
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 765 through 791
      removed outlier: 4.043A  pdb=" N   LYS A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 805
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 824 through 831
      removed outlier: 3.536A  pdb=" N   LEU A 831 " --> pdb=" O   PRO A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 839 through 843
      removed outlier: 3.758A  pdb=" N   LEU A 843 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 865 through 885
    Processing helix  chain 'A' and resid 888 through 893
    Processing helix  chain 'A' and resid 895 through 901
    Processing helix  chain 'A' and resid 916 through 946
      removed outlier: 3.597A  pdb=" N   ALA A 941 " --> pdb=" O   MET A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 961 through 981
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 995 through 1000
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1032
      removed outlier: 3.602A  pdb=" N   TYR A1032 " --> pdb=" O   ASP A1028 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 66
    Processing helix  chain 'B' and resid 103 through 118
      removed outlier: 4.589A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 121
      No H-bonds generated for 'chain 'B' and resid 119 through 121'
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 6.733A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLY B 164 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 4.166A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 190
      removed outlier: 11.912A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.401A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190
      removed outlier: 11.912A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.401A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   CYS A 258 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU A 260 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLY A 219 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR A 262 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA A 217 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN A 264 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ASP A 211 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.288A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.536A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.190A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   PHE A 594 " --> pdb=" O   GLN A 566 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLN A 566 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   THR A 503 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A 485 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.190A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLY A 596 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85
    Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 99
      removed outlier: 4.482A  pdb=" N   LEU B  94 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1521 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: 3.94

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2686
        1.33 -     1.45: 1797
        1.45 -     1.57: 5803
        1.57 -     1.69: 12
        1.69 -     1.81: 98
  Bond restraints: 10396
  Sorted by residual:
  bond pdb=" F3  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.529  1.765 -0.236 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" F2  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.535  1.752 -0.217 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" F1  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.542  1.752 -0.210 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" CG  BFD A 385 "
       pdb=" OD1 BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.269  1.446 -0.177 2.00e-02 2.50e+03 7.87e+01
  bond pdb=" C11 PCW A1105 "
       pdb=" O3  PCW A1105 "
    ideal  model  delta    sigma   weight residual
    1.326  1.455 -0.129 2.00e-02 2.50e+03 4.16e+01
  ... (remaining 10391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.32: 14004
        5.32 -    10.64: 65
       10.64 -    15.95: 4
       15.95 -    21.27: 2
       21.27 -    26.59: 3
  Bond angle restraints: 14078
  Sorted by residual:
  angle pdb=" C5  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     111.64   85.05   26.59 3.00e+00 1.11e-01 7.86e+01
  angle pdb=" C6  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     109.11   86.24   22.87 3.00e+00 1.11e-01 5.81e+01
  angle pdb=" C7  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     108.24   86.70   21.54 3.00e+00 1.11e-01 5.16e+01
  angle pdb=" F2  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     112.60   95.51   17.09 3.00e+00 1.11e-01 3.25e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F1  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     102.38  118.43  -16.05 3.00e+00 1.11e-01 2.86e+01
  ... (remaining 14073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6199
       35.81 -    71.63: 168
       71.63 -   107.44: 18
      107.44 -   143.25: 3
      143.25 -   179.07: 2
  Dihedral angle restraints: 6390
    sinusoidal: 2757
      harmonic: 3633
  Sorted by residual:
  dihedral pdb=" CA  GLY A 131 "
           pdb=" C   GLY A 131 "
           pdb=" N   ASP A 132 "
           pdb=" CA  ASP A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 152 "
           pdb=" CB  CYS B 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.65   39.35     1      1.00e+01 1.00e-02 2.18e+01
  dihedral pdb=" C33 PCW A1104 "
           pdb=" C31 PCW A1104 "
           pdb=" C32 PCW A1104 "
           pdb=" O2  PCW A1104 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -168.17   10.90 -179.07     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 6387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1290
       0.056 -    0.112: 246
       0.112 -    0.169: 23
       0.169 -    0.225: 5
       0.225 -    0.281: 3
  Chirality restraints: 1567
  Sorted by residual:
  chirality pdb=" C1  NAG B 302 "
            pdb=" ND2 ASN B  99 "
            pdb=" C2  NAG B 302 "
            pdb=" O5  NAG B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C2  PCW A1101 "
            pdb=" C1  PCW A1101 "
            pdb=" C3  PCW A1101 "
            pdb=" O2  PCW A1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.58    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C13 CLR B 305 "
            pdb=" C12 CLR B 305 "
            pdb=" C14 CLR B 305 "
            pdb=" C17 CLR B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.70   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1564 not shown)

  Planarity restraints: 1786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 303 "   -0.287 2.00e-02 2.50e+03   2.47e-01 7.62e+02
        pdb=" C7  NAG B 303 "    0.061 2.00e-02 2.50e+03
        pdb=" C8  NAG B 303 "    0.008 2.00e-02 2.50e+03
        pdb=" N2  NAG B 303 "    0.421 2.00e-02 2.50e+03
        pdb=" O7  NAG B 303 "   -0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 302 "    0.158 2.00e-02 2.50e+03   1.32e-01 2.18e+02
        pdb=" C7  NAG B 302 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG B 302 "    0.116 2.00e-02 2.50e+03
        pdb=" N2  NAG B 302 "   -0.215 2.00e-02 2.50e+03
        pdb=" O7  NAG B 302 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 304 "    0.140 2.00e-02 2.50e+03   1.15e-01 1.65e+02
        pdb=" C7  NAG B 304 "   -0.039 2.00e-02 2.50e+03
        pdb=" C8  NAG B 304 "    0.105 2.00e-02 2.50e+03
        pdb=" N2  NAG B 304 "   -0.183 2.00e-02 2.50e+03
        pdb=" O7  NAG B 304 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1783 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 166
        2.60 -     3.17: 8932
        3.17 -     3.75: 18209
        3.75 -     4.32: 25618
        4.32 -     4.90: 40020
  Nonbonded interactions: 92945
  Sorted by model distance:
  nonbonded pdb=" O   THR A 387 "
            pdb="MG    MG A1102 "
     model   vdw
     2.024 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O   HOH A1225 "
     model   vdw
     2.089 2.170
  nonbonded pdb=" OD2 ASP A 877 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" F1  BFD A 385 "
            pdb="MG    MG A1102 "
     model   vdw
     2.170 2.120
  nonbonded pdb=" OE2 GLU A 686 "
            pdb=" O   HOH A1202 "
     model   vdw
     2.183 3.040
  ... (remaining 92940 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.660
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:11.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
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      :  0.007   0.236  10402  Z= 0.344
  Angle     :  0.927  26.591  14093  Z= 0.374
  Chirality :  0.045   0.281   1567
  Planarity :  0.008   0.247   1783
  Dihedral  : 15.625 179.067   4041
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  6.20 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.40 (0.24), residues: 1244
  helix:  1.80 (0.22), residues: 578
  sheet:  0.28 (0.40), residues: 153
  loop :  0.24 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 915 
 HIS   0.002   0.001   HIS B 227 
 PHE   0.017   0.002   PHE B 284 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    3)
  link_NAG-ASN         : angle       1.86541 (    9)
  hydrogen bonds       : bond        0.12352 (  515)
  hydrogen bonds       : angle       5.53388 ( 1521)
  SS BOND              : bond        0.00491 (    3)
  SS BOND              : angle       0.68116 (    6)
  covalent geometry    : bond        0.00688 (10396)
  covalent geometry    : angle       0.92581 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 LYS cc_start: 0.8266 (tppt) cc_final: 0.7538 (tmtt)
REVERT: A  685 SER cc_start: 0.8093 (m) cc_final: 0.7648 (t)
REVERT: B   28 GLN cc_start: 0.6823 (tt0) cc_final: 0.6506 (tt0)
REVERT: B  131 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6599 (p)
REVERT: B  135 LYS cc_start: 0.7551 (mtpp) cc_final: 0.6757 (tptm)
  outliers start: 16
  outliers final: 10
  residues processed: 131
  average time/residue: 1.6056
  time to fit residues: 223.8762
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.3980
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 112 optimal weight:    7.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.169435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124493 restraints weight = 8509.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.40
r_work: 0.3214 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.0745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10402  Z= 0.172
  Angle     :  0.612  10.170  14093  Z= 0.316
  Chirality :  0.046   0.272   1567
  Planarity :  0.005   0.051   1783
  Dihedral  : 14.574 173.280   1761
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.18 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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 (0.24), residues: 1244
  helix:  1.73 (0.21), residues: 581
  sheet:  0.43 (0.40), residues: 156
  loop :  0.46 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.019   0.002   PHE B 284 
 TYR   0.019   0.002   TYR A 802 
 ARG   0.006   0.001   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01303 (    3)
  link_NAG-ASN         : angle       5.46253 (    9)
  hydrogen bonds       : bond        0.05380 (  515)
  hydrogen bonds       : angle       4.60702 ( 1521)
  SS BOND              : bond        0.00453 (    3)
  SS BOND              : angle       0.93737 (    6)
  covalent geometry    : bond        0.00369 (10396)
  covalent geometry    : angle       0.59587 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7562 (tmm-80)
REVERT: A  250 ASN cc_start: 0.8658 (p0) cc_final: 0.8417 (p0)
REVERT: A  358 LYS cc_start: 0.8602 (tppt) cc_final: 0.7968 (tmtt)
REVERT: A  455 ILE cc_start: 0.7857 (mm) cc_final: 0.7288 (tt)
REVERT: B  131 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7048 (p)
REVERT: B  135 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7242 (tptm)
  outliers start: 20
  outliers final: 11
  residues processed: 127
  average time/residue: 1.6039
  time to fit residues: 216.7695
Evaluate side-chains
  124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 123 optimal weight:    0.3980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 HIS
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.170099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.125814 restraints weight = 8616.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.34
r_work: 0.3231 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10402  Z= 0.150
  Angle     :  0.566   6.701  14093  Z= 0.295
  Chirality :  0.046   0.253   1567
  Planarity :  0.004   0.044   1783
  Dihedral  : 14.340 169.762   1760
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.30 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.54 (0.24), residues: 1244
  helix:  1.80 (0.21), residues: 581
  sheet:  0.27 (0.37), residues: 171
  loop :  0.50 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.015   0.002   PHE A 970 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.008   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00439 (    3)
  link_NAG-ASN         : angle       2.48686 (    9)
  hydrogen bonds       : bond        0.05012 (  515)
  hydrogen bonds       : angle       4.40614 ( 1521)
  SS BOND              : bond        0.00464 (    3)
  SS BOND              : angle       0.89043 (    6)
  covalent geometry    : bond        0.00321 (10396)
  covalent geometry    : angle       0.56255 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 LYS cc_start: 0.8573 (tppt) cc_final: 0.7969 (tmtt)
REVERT: A  455 ILE cc_start: 0.7930 (mm) cc_final: 0.7357 (tt)
REVERT: B   29 MET cc_start: 0.7348 (ttt) cc_final: 0.7027 (ttp)
REVERT: B  131 CYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6901 (p)
REVERT: B  135 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7254 (tptm)
REVERT: B  160 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7193 (mm-40)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 1.8180
  time to fit residues: 236.4004
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 95 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.169948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.125256 restraints weight = 8543.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.41
r_work: 0.3232 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.0945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10402  Z= 0.142
  Angle     :  0.566  11.635  14093  Z= 0.291
  Chirality :  0.045   0.255   1567
  Planarity :  0.004   0.041   1783
  Dihedral  : 14.162 168.435   1760
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.59 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.56 (0.24), residues: 1244
  helix:  1.85 (0.21), residues: 581
  sheet:  0.23 (0.37), residues: 171
  loop :  0.50 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 915 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.014   0.002   PHE A 970 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01226 (    3)
  link_NAG-ASN         : angle       5.17579 (    9)
  hydrogen bonds       : bond        0.04863 (  515)
  hydrogen bonds       : angle       4.31569 ( 1521)
  SS BOND              : bond        0.00444 (    3)
  SS BOND              : angle       0.73716 (    6)
  covalent geometry    : bond        0.00303 (10396)
  covalent geometry    : angle       0.55095 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A  358 LYS cc_start: 0.8575 (tppt) cc_final: 0.7958 (tmtt)
REVERT: A  455 ILE cc_start: 0.7985 (mm) cc_final: 0.7421 (tt)
REVERT: A  477 MET cc_start: 0.6929 (mmt) cc_final: 0.6540 (mpt)
REVERT: B  131 CYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6915 (p)
REVERT: B  135 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7249 (tptm)
REVERT: B  160 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7197 (mm-40)
  outliers start: 20
  outliers final: 14
  residues processed: 121
  average time/residue: 2.2672
  time to fit residues: 291.7687
Evaluate side-chains
  124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  160 GLN
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 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 = 0.3984 r_free = 0.3984 target = 0.170437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.125476 restraints weight = 8576.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.42
r_work: 0.3231 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.136
  Angle     :  0.543   6.743  14093  Z= 0.283
  Chirality :  0.044   0.254   1567
  Planarity :  0.004   0.039   1783
  Dihedral  : 14.046 175.865   1758
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.49 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.58 (0.24), residues: 1244
  helix:  1.88 (0.21), residues: 581
  sheet:  0.16 (0.37), residues: 171
  loop :  0.52 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 407 
 PHE   0.014   0.002   PHE A 970 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.009   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00549 (    3)
  link_NAG-ASN         : angle       2.52282 (    9)
  hydrogen bonds       : bond        0.04754 (  515)
  hydrogen bonds       : angle       4.25779 ( 1521)
  SS BOND              : bond        0.00467 (    3)
  SS BOND              : angle       0.77045 (    6)
  covalent geometry    : bond        0.00289 (10396)
  covalent geometry    : angle       0.53912 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A  455 ILE cc_start: 0.7902 (mm) cc_final: 0.7325 (tt)
REVERT: A  477 MET cc_start: 0.6863 (mmt) cc_final: 0.6523 (mpt)
REVERT: B  131 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6639 (p)
REVERT: B  135 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7287 (tptm)
  outliers start: 25
  outliers final: 16
  residues processed: 124
  average time/residue: 1.5974
  time to fit residues: 210.8389
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    0.0020
   chunk 87 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0670
   chunk 40 optimal weight:    0.0670
   chunk 69 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 106 optimal weight:    0.7980
   chunk 120 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    0.3864

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN
B 227 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.128542 restraints weight = 8656.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.44
r_work: 0.3274 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10402  Z= 0.103
  Angle     :  0.503  10.865  14093  Z= 0.255
  Chirality :  0.043   0.263   1567
  Planarity :  0.004   0.036   1783
  Dihedral  : 13.609 176.440   1758
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.43 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.76 (0.24), residues: 1244
  helix:  2.16 (0.21), residues: 572
  sheet:  0.19 (0.36), residues: 176
  loop :  0.47 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 502 
 PHE   0.015   0.001   PHE A 970 
 TYR   0.013   0.001   TYR A 802 
 ARG   0.006   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01993 (    3)
  link_NAG-ASN         : angle       5.06434 (    9)
  hydrogen bonds       : bond        0.03891 (  515)
  hydrogen bonds       : angle       4.01182 ( 1521)
  SS BOND              : bond        0.00389 (    3)
  SS BOND              : angle       0.56353 (    6)
  covalent geometry    : bond        0.00205 (10396)
  covalent geometry    : angle       0.48619 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  624 MET cc_start: 0.9253 (ttm) cc_final: 0.9010 (ttm)
REVERT: B  131 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6656 (p)
REVERT: B  135 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7249 (tptm)
  outliers start: 21
  outliers final: 16
  residues processed: 125
  average time/residue: 1.5324
  time to fit residues: 203.9946
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 405 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.170863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.125676 restraints weight = 8629.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.46
r_work: 0.3231 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.132
  Angle     :  0.542   7.040  14093  Z= 0.281
  Chirality :  0.045   0.259   1567
  Planarity :  0.004   0.037   1783
  Dihedral  : 13.579 172.922   1758
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.34 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.65 (0.24), residues: 1244
  helix:  1.95 (0.21), residues: 582
  sheet:  0.21 (0.37), residues: 171
  loop :  0.53 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 407 
 PHE   0.017   0.002   PHE A 970 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.009   0.000   ARG B 256 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00343 (    3)
  link_NAG-ASN         : angle       3.53409 (    9)
  hydrogen bonds       : bond        0.04640 (  515)
  hydrogen bonds       : angle       4.16387 ( 1521)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.61605 (    6)
  covalent geometry    : bond        0.00281 (10396)
  covalent geometry    : angle       0.53506 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.141 
Fit side-chains
REVERT: A  453 LYS cc_start: 0.8014 (mttp) cc_final: 0.7675 (mtpm)
REVERT: B  135 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7280 (tptm)
REVERT: B  256 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7869 (ttm-80)
  outliers start: 21
  outliers final: 17
  residues processed: 121
  average time/residue: 1.7208
  time to fit residues: 221.8675
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 123 optimal weight:    0.2980
   chunk 102 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.127056 restraints weight = 8628.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.33
r_work: 0.3254 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.1098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10402  Z= 0.120
  Angle     :  0.521   7.088  14093  Z= 0.271
  Chirality :  0.044   0.258   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 13.349 170.498   1758
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.62 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.67 (0.24), residues: 1244
  helix:  1.99 (0.21), residues: 581
  sheet:  0.20 (0.37), residues: 171
  loop :  0.51 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.016   0.001   PHE A 970 
 TYR   0.016   0.001   TYR A 802 
 ARG   0.008   0.000   ARG B 256 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00366 (    3)
  link_NAG-ASN         : angle       2.92729 (    9)
  hydrogen bonds       : bond        0.04396 (  515)
  hydrogen bonds       : angle       4.10587 ( 1521)
  SS BOND              : bond        0.00277 (    3)
  SS BOND              : angle       0.61138 (    6)
  covalent geometry    : bond        0.00252 (10396)
  covalent geometry    : angle       0.51551 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.243 
Fit side-chains
REVERT: A  686 GLU cc_start: 0.8049 (mt-10) cc_final: 0.6981 (tp30)
REVERT: B  135 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7288 (tptm)
REVERT: B  256 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7840 (ttm-80)
  outliers start: 20
  outliers final: 17
  residues processed: 122
  average time/residue: 2.2417
  time to fit residues: 292.2408
Evaluate side-chains
  124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0470
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.172304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127399 restraints weight = 8721.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.46
r_work: 0.3258 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10402  Z= 0.108
  Angle     :  0.518  10.678  14093  Z= 0.263
  Chirality :  0.043   0.276   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 13.025 168.845   1758
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.71 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.77 (0.24), residues: 1244
  helix:  2.08 (0.21), residues: 577
  sheet:  0.38 (0.37), residues: 163
  loop :  0.50 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.016   0.001   PHE A 970 
 TYR   0.014   0.001   TYR A 802 
 ARG   0.007   0.000   ARG B 256 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01126 (    3)
  link_NAG-ASN         : angle       5.44530 (    9)
  hydrogen bonds       : bond        0.04093 (  515)
  hydrogen bonds       : angle       4.01720 ( 1521)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       1.06135 (    6)
  covalent geometry    : bond        0.00222 (10396)
  covalent geometry    : angle       0.49959 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.219 
Fit side-chains
REVERT: A  686 GLU cc_start: 0.8052 (mt-10) cc_final: 0.6934 (tp30)
REVERT: B   29 MET cc_start: 0.7489 (ttt) cc_final: 0.7192 (ttp)
REVERT: B  135 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7264 (tptm)
REVERT: B  256 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7840 (ttm-80)
  outliers start: 17
  outliers final: 16
  residues processed: 119
  average time/residue: 1.6986
  time to fit residues: 215.2549
Evaluate side-chains
  119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0050
   chunk 56 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0570
   chunk 2 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.0118

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125812 restraints weight = 8588.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.45
r_work: 0.3232 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.134
  Angle     :  0.545   7.163  14093  Z= 0.283
  Chirality :  0.045   0.321   1567
  Planarity :  0.004   0.036   1783
  Dihedral  : 13.169 169.596   1758
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.43 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.67 (0.24), residues: 1244
  helix:  1.98 (0.21), residues: 577
  sheet:  0.20 (0.37), residues: 171
  loop :  0.54 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  39 
 HIS   0.003   0.001   HIS A 407 
 PHE   0.018   0.002   PHE A 970 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.007   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00498 (    3)
  link_NAG-ASN         : angle       3.38937 (    9)
  hydrogen bonds       : bond        0.04652 (  515)
  hydrogen bonds       : angle       4.15130 ( 1521)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       0.59137 (    6)
  covalent geometry    : bond        0.00285 (10396)
  covalent geometry    : angle       0.53862 (14078)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A  287 GLU cc_start: 0.7431 (pm20) cc_final: 0.6955 (mm-30)
REVERT: A  453 LYS cc_start: 0.8009 (mttp) cc_final: 0.7669 (mtpm)
REVERT: A  686 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6960 (tp30)
REVERT: B   29 MET cc_start: 0.7472 (ttt) cc_final: 0.7175 (ttp)
REVERT: B  135 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7280 (tptm)
REVERT: B  256 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7825 (ttm-80)
  outliers start: 21
  outliers final: 18
  residues processed: 121
  average time/residue: 1.6086
  time to fit residues: 207.8822
Evaluate side-chains
  122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 ASP
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  287 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0370
   chunk 27 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125832 restraints weight = 8597.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.45
r_work: 0.3235 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.131
  Angle     :  0.554  10.220  14093  Z= 0.283
  Chirality :  0.045   0.350   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 13.194 169.734   1758
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.09 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.69 (0.24), residues: 1244
  helix:  1.98 (0.21), residues: 577
  sheet:  0.35 (0.37), residues: 163
  loop :  0.51 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  39 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.019   0.002   PHE A 333 
 TYR   0.017   0.002   TYR A 802 
 ARG   0.008   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01312 (    3)
  link_NAG-ASN         : angle       5.63162 (    9)
  hydrogen bonds       : bond        0.04608 (  515)
  hydrogen bonds       : angle       4.15089 ( 1521)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.70011 (    6)
  covalent geometry    : bond        0.00277 (10396)
  covalent geometry    : angle       0.53565 (14078)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13109.44 seconds
wall clock time: 231 minutes 51.26 seconds (13911.26 seconds total)