Starting phenix.real_space_refine
on Tue May 13 23:45:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ijx_35502/05_2025/8ijx_35502.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ijx_35502/05_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_35502/05_2025/8ijx_35502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ijx_35502/05_2025/8ijx_35502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ijx_35502/05_2025/8ijx_35502.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ijx_35502/05_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-5687/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: 7.97, per 1000 atoms: 0.76
  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: 3.14
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.60
  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: 4.27

  Time building geometry restraints manager: 3.55 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:                  0.010
  Normalize map: mean=0, sd=1:             5.510
  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:         0.080
  Set scattering table:                    0.090
  Process input model:                     31.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.770
-------------------------------------------------------------------------------
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  : 1.128 
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: 1.5602
  time to fit residues: 217.4211
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  : 1.180 
-------------------------------------------------------------------------------
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 = 0.124503 restraints weight = 8509.852|
|-----------------------------------------------------------------------------|
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: 0.3103 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
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  10.171  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       5.46248 (    9)
  hydrogen bonds       : bond        0.05380 (  515)
  hydrogen bonds       : angle       4.60701 ( 1521)
  SS BOND              : bond        0.00453 (    3)
  SS BOND              : angle       0.93735 (    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  : 1.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7575 (tmm-80)
REVERT: A  250 ASN cc_start: 0.8661 (p0) cc_final: 0.8421 (p0)
REVERT: A  358 LYS cc_start: 0.8601 (tppt) cc_final: 0.7972 (tmtt)
REVERT: A  455 ILE cc_start: 0.7868 (mm) cc_final: 0.7304 (tt)
REVERT: B  131 CYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7038 (p)
REVERT: B  135 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7245 (tptm)
  outliers start: 20
  outliers final: 11
  residues processed: 127
  average time/residue: 1.6201
  time to fit residues: 218.8051
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  : 1.127 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 43 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.170055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.125776 restraints weight = 8612.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.34
r_work: 0.3230 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.0861

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= 0.151
  Angle     :  0.568   6.718  14093  Z= 0.296
  Chirality :  0.046   0.262   1567
  Planarity :  0.004   0.044   1783
  Dihedral  : 14.341 169.595   1760
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  9.21 %
    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:  1.53 (0.24), residues: 1244
  helix:  1.79 (0.21), residues: 581
  sheet:  0.27 (0.38), 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        0.00577 (    3)
  link_NAG-ASN         : angle       2.52883 (    9)
  hydrogen bonds       : bond        0.05034 (  515)
  hydrogen bonds       : angle       4.40921 ( 1521)
  SS BOND              : bond        0.00458 (    3)
  SS BOND              : angle       0.84758 (    6)
  covalent geometry    : bond        0.00324 (10396)
  covalent geometry    : angle       0.56395 (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
  130 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 LYS cc_start: 0.8568 (tppt) cc_final: 0.7972 (tmtt)
REVERT: A  455 ILE cc_start: 0.7944 (mm) cc_final: 0.7372 (tt)
REVERT: B   29 MET cc_start: 0.7353 (ttt) cc_final: 0.7034 (ttp)
REVERT: B  131 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6843 (p)
REVERT: B  135 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7256 (tptm)
REVERT: B  160 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7192 (mm-40)
  outliers start: 19
  outliers final: 13
  residues processed: 123
  average time/residue: 1.6707
  time to fit residues: 218.6253
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  : 1.228 
-------------------------------------------------------------------------------
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 92 optimal weight:    0.3980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3988 r_free = 0.3988 target = 0.170757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125779 restraints weight = 8538.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.44
r_work: 0.3232 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.0924

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= 0.130
  Angle     :  0.549  11.454  14093  Z= 0.282
  Chirality :  0.044   0.258   1567
  Planarity :  0.004   0.041   1783
  Dihedral  : 14.053 167.974   1758
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.68 %
    Favored  : 88.63 %
  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: 582
  sheet:  0.25 (0.37), residues: 171
  loop :  0.46 (0.28), residues: 491

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   0.013   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        0.01194 (    3)
  link_NAG-ASN         : angle       5.35421 (    9)
  hydrogen bonds       : bond        0.04644 (  515)
  hydrogen bonds       : angle       4.25811 ( 1521)
  SS BOND              : bond        0.00431 (    3)
  SS BOND              : angle       0.67116 (    6)
  covalent geometry    : bond        0.00273 (10396)
  covalent geometry    : angle       0.53246 (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
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 1.145 
Fit side-chains
REVERT: A  358 LYS cc_start: 0.8559 (tppt) cc_final: 0.7954 (tmtt)
REVERT: A  455 ILE cc_start: 0.7900 (mm) cc_final: 0.7351 (tt)
REVERT: A  477 MET cc_start: 0.6913 (mmt) cc_final: 0.6570 (mpt)
REVERT: B  131 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6849 (p)
REVERT: B  135 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7243 (tptm)
REVERT: B  160 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7211 (mm-40)
  outliers start: 18
  outliers final: 13
  residues processed: 120
  average time/residue: 1.5567
  time to fit residues: 199.1019
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
B 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.171026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.126379 restraints weight = 8610.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.42
r_work: 0.3249 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10402  Z= 0.119
  Angle     :  0.519   6.745  14093  Z= 0.270
  Chirality :  0.044   0.254   1567
  Planarity :  0.004   0.038   1783
  Dihedral  : 13.872 174.611   1758
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.06 %
    Favored  : 87.88 %
  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:  1.61 (0.24), residues: 1244
  helix:  1.93 (0.21), residues: 582
  sheet:  0.21 (0.37), residues: 171
  loop :  0.48 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 915 
 HIS   0.002   0.001   HIS A 629 
 PHE   0.014   0.001   PHE A 970 
 TYR   0.016   0.001   TYR A 802 
 ARG   0.008   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00475 (    3)
  link_NAG-ASN         : angle       2.25388 (    9)
  hydrogen bonds       : bond        0.04447 (  515)
  hydrogen bonds       : angle       4.17213 ( 1521)
  SS BOND              : bond        0.00425 (    3)
  SS BOND              : angle       0.59550 (    6)
  covalent geometry    : bond        0.00249 (10396)
  covalent geometry    : angle       0.51567 (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: 22
    poor density    : 109
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A  358 LYS cc_start: 0.8543 (tppt) cc_final: 0.7950 (tmtt)
REVERT: A  477 MET cc_start: 0.6843 (mmt) cc_final: 0.6490 (mpt)
REVERT: B  131 CYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6559 (p)
REVERT: B  135 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7257 (tptm)
  outliers start: 22
  outliers final: 14
  residues processed: 125
  average time/residue: 1.5109
  time to fit residues: 201.3021
Evaluate side-chains
  121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   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 = 0.3992 r_free = 0.3992 target = 0.171131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126079 restraints weight = 8609.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.45
r_work: 0.3239 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.1006

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= 0.121
  Angle     :  0.533  10.061  14093  Z= 0.273
  Chirality :  0.044   0.252   1567
  Planarity :  0.004   0.037   1783
  Dihedral  : 13.770 179.765   1758
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.24 %
    Favored  : 87.78 %
  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:  1.63 (0.24), residues: 1244
  helix:  1.94 (0.21), residues: 582
  sheet:  0.19 (0.37), residues: 171
  loop :  0.49 (0.28), residues: 491

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   0.015   0.001   PHE A 970 
 TYR   0.016   0.001   TYR A 802 
 ARG   0.007   0.000   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01480 (    3)
  link_NAG-ASN         : angle       5.02130 (    9)
  hydrogen bonds       : bond        0.04445 (  515)
  hydrogen bonds       : angle       4.14858 ( 1521)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       0.95824 (    6)
  covalent geometry    : bond        0.00252 (10396)
  covalent geometry    : angle       0.51808 (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
  130 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.283 
Fit side-chains
REVERT: A  477 MET cc_start: 0.6825 (mmt) cc_final: 0.6546 (mpt)
REVERT: B  135 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7266 (tptm)
  outliers start: 21
  outliers final: 19
  residues processed: 125
  average time/residue: 1.5177
  time to fit residues: 202.5062
Evaluate side-chains
  124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
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  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  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:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.170838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.126648 restraints weight = 8645.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.37
r_work: 0.3244 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1039

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= 0.129
  Angle     :  0.533   6.979  14093  Z= 0.277
  Chirality :  0.044   0.249   1567
  Planarity :  0.004   0.038   1783
  Dihedral  : 13.627 174.840   1758
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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:  1.60 (0.24), residues: 1244
  helix:  1.90 (0.21), residues: 582
  sheet:  0.18 (0.37), residues: 171
  loop :  0.50 (0.28), residues: 491

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   0.015   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        0.00356 (    3)
  link_NAG-ASN         : angle       2.79379 (    9)
  hydrogen bonds       : bond        0.04594 (  515)
  hydrogen bonds       : angle       4.17375 ( 1521)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.53383 (    6)
  covalent geometry    : bond        0.00271 (10396)
  covalent geometry    : angle       0.52826 (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  : 1.262 
Fit side-chains
REVERT: A  477 MET cc_start: 0.6831 (mmt) cc_final: 0.6585 (mpt)
REVERT: B  135 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7279 (tptm)
REVERT: B  256 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7829 (ttm-80)
  outliers start: 21
  outliers final: 19
  residues processed: 123
  average time/residue: 1.5202
  time to fit residues: 199.4891
Evaluate side-chains
  126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
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  585 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.168914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.124788 restraints weight = 8561.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.38
r_work: 0.3214 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10402  Z= 0.186
  Angle     :  0.620  10.113  14093  Z= 0.320
  Chirality :  0.047   0.272   1567
  Planarity :  0.005   0.040   1783
  Dihedral  : 13.987 173.862   1758
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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:  1.45 (0.23), residues: 1244
  helix:  1.72 (0.21), residues: 581
  sheet:  0.14 (0.37), residues: 171
  loop :  0.50 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.017   0.002   PHE B 284 
 TYR   0.020   0.002   TYR A 802 
 ARG   0.008   0.001   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01513 (    3)
  link_NAG-ASN         : angle       5.30094 (    9)
  hydrogen bonds       : bond        0.05412 (  515)
  hydrogen bonds       : angle       4.41350 ( 1521)
  SS BOND              : bond        0.00521 (    3)
  SS BOND              : angle       0.79985 (    6)
  covalent geometry    : bond        0.00407 (10396)
  covalent geometry    : angle       0.60587 (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: 21
    poor density    : 107
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A  287 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6925 (mm-30)
REVERT: B  256 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7863 (ttm-80)
  outliers start: 21
  outliers final: 17
  residues processed: 122
  average time/residue: 1.4840
  time to fit residues: 193.5094
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  : 1.261 
-------------------------------------------------------------------------------
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.169209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.124275 restraints weight = 8684.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.45
r_work: 0.3212 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1114

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= 0.160
  Angle     :  0.580   7.021  14093  Z= 0.303
  Chirality :  0.046   0.292   1567
  Planarity :  0.004   0.038   1783
  Dihedral  : 13.896 172.717   1758
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.00 %
    Favored  : 87.12 %
  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 (0.23), residues: 1244
  helix:  1.79 (0.21), residues: 577
  sheet:  0.12 (0.37), residues: 171
  loop :  0.51 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.015   0.002   PHE A 315 
 TYR   0.018   0.002   TYR A 802 
 ARG   0.007   0.001   ARG A 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00608 (    3)
  link_NAG-ASN         : angle       3.50570 (    9)
  hydrogen bonds       : bond        0.05107 (  515)
  hydrogen bonds       : angle       4.33911 ( 1521)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       0.64924 (    6)
  covalent geometry    : bond        0.00348 (10396)
  covalent geometry    : angle       0.57371 (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
  127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  287 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6917 (mm-30)
REVERT: A  477 MET cc_start: 0.6958 (mmt) cc_final: 0.6592 (mpt)
REVERT: B  256 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7864 (ttm-80)
  outliers start: 20
  outliers final: 17
  residues processed: 122
  average time/residue: 1.4787
  time to fit residues: 192.6481
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 
-------------------------------------------------------------------------------
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    0.2980
   chunk 75 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 119 optimal weight:    0.0670
   chunk 56 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 2 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.5720

-------------------------------------------------------------------------------
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 227 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.171611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126832 restraints weight = 8629.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.44
r_work: 0.3249 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1125

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= 0.113
  Angle     :  0.528  11.288  14093  Z= 0.269
  Chirality :  0.044   0.268   1567
  Planarity :  0.004   0.036   1783
  Dihedral  : 13.464 169.330   1758
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.09 %
    Favored  : 87.41 %
  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:  1.64 (0.24), residues: 1244
  helix:  1.99 (0.21), residues: 578
  sheet:  0.13 (0.37), residues: 171
  loop :  0.50 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.003   0.001   HIS A 629 
 PHE   0.014   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        0.01677 (    3)
  link_NAG-ASN         : angle       5.50430 (    9)
  hydrogen bonds       : bond        0.04248 (  515)
  hydrogen bonds       : angle       4.10988 ( 1521)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       0.57482 (    6)
  covalent geometry    : bond        0.00230 (10396)
  covalent geometry    : angle       0.50956 (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
  121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  453 LYS cc_start: 0.7999 (mttp) cc_final: 0.7654 (mtpm)
REVERT: A  477 MET cc_start: 0.6865 (mmt) cc_final: 0.6546 (mpt)
REVERT: B   29 MET cc_start: 0.7471 (ttt) cc_final: 0.7176 (ttp)
  outliers start: 16
  outliers final: 15
  residues processed: 119
  average time/residue: 1.6191
  time to fit residues: 204.8628
Evaluate side-chains
  118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.0782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.170140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125082 restraints weight = 8571.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.41
r_work: 0.3228 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1153

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= 0.141
  Angle     :  0.569  11.445  14093  Z= 0.292
  Chirality :  0.045   0.255   1567
  Planarity :  0.004   0.035   1783
  Dihedral  : 13.508 169.672   1756
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.90 %
    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:  1.59 (0.24), residues: 1244
  helix:  1.89 (0.21), residues: 577
  sheet:  0.12 (0.36), residues: 171
  loop :  0.55 (0.28), residues: 496

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   0.016   0.002   PHE A 970 
 TYR   0.018   0.002   TYR A 802 
 ARG   0.005   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01016 (    3)
  link_NAG-ASN         : angle       5.66062 (    9)
  hydrogen bonds       : bond        0.04839 (  515)
  hydrogen bonds       : angle       4.23215 ( 1521)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.58921 (    6)
  covalent geometry    : bond        0.00300 (10396)
  covalent geometry    : angle       0.55123 (14078)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11943.13 seconds
wall clock time: 205 minutes 34.12 seconds (12334.12 seconds total)