Starting phenix.real_space_refine
on Thu Aug  6 18:15:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ihd_52865/08_2026/9ihd_52865.map"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P     290      5.49       5
     S      41      5.16       5
     C    9483      2.51       5
     N    3075      2.21       5
     O    3618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16508
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 795
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 825
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "M"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 806
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 9, 'TRANS': 90}
    Chain: "N"
      Number of atoms: 3670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3670
          Classifications: {'peptide': 457}
          Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420}
    Chain: "N"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 85
          Unusual residues: {'HEM': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.98, per 1000 atoms: 0.18
  Number of scatterers: 16508
  At special positions: 0
  Unit cell: (119.68, 121.04, 133.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      1     26.01
     S      41     16.00
     P     290     15.00
     O    3618      8.00
     N    3075      7.00
     C    9483      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N 221 " - pdb=" SG  CYS N 232 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 440 " - pdb=" SG  CYS N 497 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 538 " - pdb=" SG  CYS N 564 " 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=3, symmetry=0
  Links applied
    NAG-ASN
      " NAG N 603 " - " ASN N 189 "
      " NAG N 604 " - " ASN N 317 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 466.3 milliseconds
  

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2464

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 14 sheets defined
      60.6% alpha, 3.0% beta
      134 base pairs and 263 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.121A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.547A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.877A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.994A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.506A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.671A  pdb=" N   VAL D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.505A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.560A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.860A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.560A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.720A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.700A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 60 through 68
    Processing helix  chain 'M' and resid 72 through 76
    Processing helix  chain 'M' and resid 84 through 98
    Processing helix  chain 'N' and resid 180 through 188
    Processing helix  chain 'N' and resid 219 through 225
      removed outlier: 3.951A  pdb=" N   LEU N 223 " --> pdb=" O   ASP N 219 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR N 224 " --> pdb=" O   PRO N 220 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN N 225 " --> pdb=" O   CYS N 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 219 through 225'
    Processing helix  chain 'N' and resid 243 through 268
    Processing helix  chain 'N' and resid 272 through 310
      removed outlier: 5.312A  pdb=" N   LEU N 297 " --> pdb=" O   TYR N 293 " (cutoff:3.500A)
      Proline residue:  N 298  - end of helix
      Proline residue:  N 303  - end of helix
    Processing helix  chain 'N' and resid 327 through 332
    Processing helix  chain 'N' and resid 333 through 338
    Processing helix  chain 'N' and resid 362 through 364
      No H-bonds generated for 'chain 'N' and resid 362 through 364'
    Processing helix  chain 'N' and resid 368 through 373
      removed outlier: 3.601A  pdb=" N   VAL N 372 " --> pdb=" O   SER N 368 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 377 through 386
    Processing helix  chain 'N' and resid 399 through 405
    Processing helix  chain 'N' and resid 416 through 428
    Processing helix  chain 'N' and resid 432 through 440
    Processing helix  chain 'N' and resid 447 through 456
    Processing helix  chain 'N' and resid 457 through 469
      removed outlier: 3.672A  pdb=" N   ALA N 461 " --> pdb=" O   ASN N 457 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 470 through 474
    Processing helix  chain 'N' and resid 475 through 483
    Processing helix  chain 'N' and resid 492 through 509
    Processing helix  chain 'N' and resid 521 through 529
    Processing helix  chain 'N' and resid 532 through 541
      removed outlier: 3.633A  pdb=" N   THR N 541 " --> pdb=" O   ILE N 537 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 571 through 576
      removed outlier: 4.210A  pdb=" N   SER N 574 " --> pdb=" O   ASN N 571 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG N 576 " --> pdb=" O   ALA N 573 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.151A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.160A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.725A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.010A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.158A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'M' and resid 27 through 28
      removed outlier: 3.692A  pdb=" N   ARG M  27 " --> pdb=" O   ASN N 165 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 52 through 53
    Processing sheet with id=AB3, first strand: chain 'M' and resid 78 through 83
      removed outlier: 3.970A  pdb=" N   ALA N 389 " --> pdb=" O   ASP M  79 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 342 through 344
    Processing sheet with id=AB5, first strand: chain 'N' and resid 546 through 547

    555 hydrogen bonds defined for protein.
    1617 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      345 hydrogen bonds
      686 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      263 stacking parallelities
  Total time for adding SS restraints: 3.65

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 6760
        1.39 -     1.57: 10016
        1.57 -     1.75: 578
        1.75 -     1.93: 69
        1.93 -     2.11: 4
  Bond restraints: 17427
  Sorted by residual:
  bond pdb=" C3'  DA I -30 "
       pdb=" C2'  DA I -30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.47e+01
  bond pdb=" C3'  DC J  44 "
       pdb=" C2'  DC J  44 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.74e+00
  bond pdb=" C3'  DC I -40 "
       pdb=" C2'  DC I -40 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.06e+00
  bond pdb=" C3'  DA J  63 "
       pdb=" C2'  DA J  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.92e+00
  bond pdb=" C3'  DC J -21 "
       pdb=" C2'  DC J -21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.34e+00
  ... (remaining 17422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 24684
        2.88 -     5.77: 129
        5.77 -     8.65: 8
        8.65 -    11.53: 3
       11.53 -    14.41: 2
  Bond angle restraints: 24826
  Sorted by residual:
  angle pdb=" O4'  DC J -48 "
        pdb=" C4'  DC J -48 "
        pdb=" C3'  DC J -48 "
      ideal   model   delta    sigma   weight residual
     106.00  103.09    2.91 6.00e-01 2.78e+00 2.36e+01
  angle pdb=" N   ASN N 189 "
        pdb=" CA  ASN N 189 "
        pdb=" C   ASN N 189 "
      ideal   model   delta    sigma   weight residual
     110.65  104.72    5.93 1.26e+00 6.30e-01 2.21e+01
  angle pdb=" O4'  DG J -49 "
        pdb=" C4'  DG J -49 "
        pdb=" C3'  DG J -49 "
      ideal   model   delta    sigma   weight residual
     106.00  103.22    2.78 6.00e-01 2.78e+00 2.15e+01
  angle pdb=" N3   DT J -42 "
        pdb=" C4   DT J -42 "
        pdb=" O4   DT J -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT I  31 "
        pdb=" C4   DT I  31 "
        pdb=" O4   DT I  31 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.96e+01
  ... (remaining 24821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.32: 8241
       35.32 -    70.65: 1542
       70.65 -   105.97: 17
      105.97 -   141.30: 2
      141.30 -   176.62: 6
  Dihedral angle restraints: 9808
    sinusoidal: 5996
      harmonic: 3812
  Sorted by residual:
  dihedral pdb=" C4'  DC J  44 "
           pdb=" C3'  DC J  44 "
           pdb=" O3'  DC J  44 "
           pdb=" P    DC J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.62 -176.62     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J -21 "
           pdb=" C3'  DC J -21 "
           pdb=" O3'  DC J -21 "
           pdb=" P    DC J -20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.93  165.07     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA J -31 "
           pdb=" C3'  DA J -31 "
           pdb=" O3'  DA J -31 "
           pdb=" P    DG J -30 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.87  156.13     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 9805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 2768
       0.125 -    0.249: 14
       0.249 -    0.374: 0
       0.374 -    0.499: 0
       0.499 -    0.623: 1
  Chirality restraints: 2783
  Sorted by residual:
  chirality pdb=" C1  NAG N 603 "
            pdb=" ND2 ASN N 189 "
            pdb=" C2  NAG N 603 "
            pdb=" O5  NAG N 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.78   -0.62 2.00e-01 2.50e+01 9.72e+00
  chirality pdb=" C3'  DC J  44 "
            pdb=" C4'  DC J  44 "
            pdb=" O3'  DC J  44 "
            pdb=" C2'  DC J  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  GLU M  67 "
            pdb=" N   GLU M  67 "
            pdb=" C   GLU M  67 "
            pdb=" CB  GLU M  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 2780 not shown)

  Planarity restraints: 2171
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 333 "   -0.522 9.50e-02 1.11e+02   2.34e-01 3.36e+01
        pdb=" NE  ARG N 333 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 333 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 333 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 333 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN N 189 "   -0.026 2.00e-02 2.50e+03   2.52e-02 7.93e+00
        pdb=" CG  ASN N 189 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN N 189 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN N 189 "    0.026 2.00e-02 2.50e+03
        pdb=" C1  NAG N 603 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H 108 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   VAL H 108 "    0.030 2.00e-02 2.50e+03
        pdb=" O   VAL H 108 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER H 109 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 2168 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 875
        2.72 -     3.27: 14329
        3.27 -     3.81: 30007
        3.81 -     4.36: 37841
        4.36 -     4.90: 56974
  Nonbonded interactions: 140026
  Sorted by model distance:
  nonbonded pdb=" O   ASN C  73 "
            pdb=" ND2 ASN C  73 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   THR C  76 "
            pdb=" OG1 THR C  76 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NH1 ARG M  62 "
            pdb=" OD2 ASP N 416 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NH2 ARG N 333 "
            pdb=" O2A HEM N 601 "
     model   vdw
     2.264 2.496
  nonbonded pdb=" OG1 THR B  73 "
            pdb=" OD2 ASP B  85 "
     model   vdw
     2.266 3.040
  ... (remaining 140021 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 11 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.100
  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:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.590
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
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      :  0.006   0.425  17435  Z= 0.444
  Angle     :  0.724  14.414  24838  Z= 0.590
  Chirality :  0.044   0.623   2783
  Planarity :  0.007   0.234   2169
  Dihedral  : 26.624 176.619   7335
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 23.90 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.24), residues: 1293
  helix:  1.90 (0.20), residues: 737
  sheet:  None (None), residues: 0
  loop : -0.17 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG N 185 
 TYR   0.010   0.001   TYR D  34 
 PHE   0.009   0.001   PHE N 332 
 TRP   0.007   0.001   TRP M  89 
 HIS   0.002   0.000   HIS M  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.44 (17427)
  covalent geometry    : angle       0.71850 /  0.59 (24826)
  SS BOND              : bond        0.00208 /  0.12 (    3)
  SS BOND              : angle       0.80055 /  0.43 (    6)
  hydrogen bonds       : bond        0.12352 /  8.48 (  900)
  hydrogen bonds       : angle       4.69170 /  3.35 ( 2303)
  Misc. bond           : bond        0.24531 / 11.68 (    3)
  link_NAG-ASN         : bond        0.01147 /  0.76 (    2)
  link_NAG-ASN         : angle       6.00863 /  3.63 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8352 (tttt) cc_final: 0.7925 (tttm)
REVERT: A  115 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8145 (mttp)
REVERT: A  129 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7210 (tmt170)
REVERT: C   15 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8140 (ptmm)
REVERT: D   32 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7286 (pt0)
REVERT: E   59 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7912 (pt0)
REVERT: E  120 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8272 (mtt)
REVERT: F   44 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8435 (tttm)
REVERT: G   74 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8385 (mtmm)
REVERT: G   95 LYS cc_start: 0.8766 (tttt) cc_final: 0.8382 (ttmt)
REVERT: G  108 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8610 (mp)
REVERT: H   83 ARG cc_start: 0.8451 (mmt-90) cc_final: 0.7996 (mmt90)
REVERT: M   27 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8453 (mtp85)
REVERT: M   67 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7456 (pm20)
REVERT: N  140 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (tt0)
REVERT: N  185 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7866 (ttp-110)
REVERT: N  210 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: N  249 MET cc_start: 0.8813 (mmm) cc_final: 0.8579 (mmt)
REVERT: N  462 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7915 (mtt90)
REVERT: N  504 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (ttt180)
REVERT: N  526 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6859 (mp10)
  outliers start: 31
  outliers final: 18
  residues processed: 166
  average time/residue: 0.7218
  time to fit residues: 131.0575
Evaluate side-chains
  168 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain M residue   67 GLU
Chi-restraints excluded: chain N residue  140 GLN
Chi-restraints excluded: chain N residue  158 ILE
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  504 ARG
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  547 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    0.0060
   overall best weight:    1.3598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
B  75 HIS
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.158235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.121048 restraints weight = 17809.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.24
r_work: 0.3340 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.0550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.374  17435  Z= 0.161
  Angle     :  0.643  16.376  24838  Z= 0.349
  Chirality :  0.047   0.544   2783
  Planarity :  0.005   0.091   2169
  Dihedral  : 29.015 174.756   4769
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.11 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.23), residues: 1293
  helix:  2.20 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.29 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N 185 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.008   0.001   TRP N 436 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.16 (17427)
  covalent geometry    : angle       0.63434 /  0.35 (24826)
  SS BOND              : bond        0.00349 /  0.20 (    3)
  SS BOND              : angle       0.53240 /  0.35 (    6)
  hydrogen bonds       : bond        0.05361 /  3.61 (  900)
  hydrogen bonds       : angle       3.46428 /  2.50 ( 2303)
  Misc. bond           : bond        0.21620 / 10.30 (    3)
  link_NAG-ASN         : bond        0.01863 /  1.24 (    2)
  link_NAG-ASN         : angle       6.77477 /  4.03 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8043 (tttt) cc_final: 0.7657 (tttm)
REVERT: A  129 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7919 (tmt170)
REVERT: C   15 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8169 (ptmm)
REVERT: D   32 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7264 (pt0)
REVERT: E  131 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7423 (mtp85)
REVERT: F   92 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7921 (ttp80)
REVERT: G   74 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8367 (mtmm)
REVERT: G   92 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7495 (mm-30)
REVERT: G   95 LYS cc_start: 0.8803 (tttt) cc_final: 0.8554 (ttmt)
REVERT: G  108 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: H   83 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.8380 (mmt-90)
REVERT: H   90 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7764 (mp0)
REVERT: M   27 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8243 (mtp85)
REVERT: N  210 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7237 (mp)
REVERT: N  249 MET cc_start: 0.8658 (mmm) cc_final: 0.8424 (mmt)
REVERT: N  319 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8115 (t)
REVERT: N  526 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (mp10)
  outliers start: 38
  outliers final: 12
  residues processed: 173
  average time/residue: 0.7192
  time to fit residues: 136.2088
Evaluate side-chains
  163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  319 SER
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  427 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 47 optimal weight:    1.9990
   chunk 152 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 153 optimal weight:    3.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.159251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.122303 restraints weight = 17973.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.22
r_work: 0.3353 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.0694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.360  17435  Z= 0.142
  Angle     :  0.607  15.248  24838  Z= 0.332
  Chirality :  0.045   0.445   2783
  Planarity :  0.004   0.089   2169
  Dihedral  : 29.082 173.208   4720
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.56 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.24), residues: 1293
  helix:  2.43 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -0.28 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 148 
 TYR   0.009   0.001   TYR D  34 
 PHE   0.008   0.001   PHE M  86 
 TRP   0.007   0.001   TRP N 436 
 HIS   0.002   0.001   HIS N 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 (17427)
  covalent geometry    : angle       0.59912 /  0.33 (24826)
  SS BOND              : bond        0.00319 /  0.19 (    3)
  SS BOND              : angle       0.56631 /  0.39 (    6)
  hydrogen bonds       : bond        0.04930 /  3.33 (  900)
  hydrogen bonds       : angle       3.28484 /  2.38 ( 2303)
  Misc. bond           : bond        0.20798 /  9.90 (    3)
  link_NAG-ASN         : bond        0.01493 /  1.00 (    2)
  link_NAG-ASN         : angle       6.21894 /  3.62 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7971 (tttt) cc_final: 0.7592 (tttm)
REVERT: A  129 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7939 (tmt170)
REVERT: C   15 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8135 (ptmm)
REVERT: D   32 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7274 (pt0)
REVERT: F   92 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7921 (ttp80)
REVERT: G   74 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8333 (mtmm)
REVERT: G   92 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7481 (mm-30)
REVERT: G   95 LYS cc_start: 0.8786 (tttt) cc_final: 0.8540 (ttmt)
REVERT: G  108 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8646 (mp)
REVERT: H   83 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8369 (mmt-90)
REVERT: H   90 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7806 (mp0)
REVERT: M   27 ARG cc_start: 0.8821 (mmm160) cc_final: 0.8299 (mtp85)
REVERT: M   52 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7378 (mttp)
REVERT: M   53 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7210 (ttm170)
REVERT: N  185 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7790 (ttp-110)
REVERT: N  210 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7225 (mp)
REVERT: N  249 MET cc_start: 0.8613 (mmm) cc_final: 0.8391 (mmt)
REVERT: N  319 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8096 (t)
  outliers start: 37
  outliers final: 15
  residues processed: 167
  average time/residue: 0.7268
  time to fit residues: 132.2019
Evaluate side-chains
  165 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  319 SER
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 133 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 138 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.155569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.118080 restraints weight = 17694.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.24
r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.333  17435  Z= 0.228
  Angle     :  0.671  16.778  24838  Z= 0.356
  Chirality :  0.049   0.427   2783
  Planarity :  0.005   0.115   2169
  Dihedral  : 29.328 174.432   4716
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 20.95 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.23), residues: 1293
  helix:  2.20 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.48 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 202 
 TYR   0.014   0.001   TYR D  34 
 PHE   0.010   0.002   PHE H  62 
 TRP   0.008   0.001   TRP N 436 
 HIS   0.003   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.23 (17427)
  covalent geometry    : angle       0.66488 /  0.35 (24826)
  SS BOND              : bond        0.00410 /  0.23 (    3)
  SS BOND              : angle       0.65158 /  0.46 (    6)
  hydrogen bonds       : bond        0.05923 /  4.00 (  900)
  hydrogen bonds       : angle       3.36611 /  2.44 ( 2303)
  Misc. bond           : bond        0.19214 /  9.15 (    3)
  link_NAG-ASN         : bond        0.01198 /  0.80 (    2)
  link_NAG-ASN         : angle       5.89707 /  3.43 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 136
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8050 (tttt) cc_final: 0.7708 (tttm)
REVERT: A  129 ARG cc_start: 0.8233 (ttt180) cc_final: 0.7932 (tmt170)
REVERT: C   15 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8176 (ptmm)
REVERT: D   32 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7297 (pt0)
REVERT: E   59 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8046 (pt0)
REVERT: E  131 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7404 (mtp85)
REVERT: G   74 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8345 (mtmm)
REVERT: G   92 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7605 (mm-30)
REVERT: G   95 LYS cc_start: 0.8816 (tttt) cc_final: 0.8569 (ttmt)
REVERT: G  108 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8656 (mp)
REVERT: H   30 ARG cc_start: 0.8010 (mmt90) cc_final: 0.6763 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.8445 (mmt-90)
REVERT: H   90 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7839 (mp0)
REVERT: M   27 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8248 (mtp85)
REVERT: M   52 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7431 (mttp)
REVERT: N  210 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7194 (mp)
REVERT: N  249 MET cc_start: 0.8671 (mmm) cc_final: 0.8430 (mmt)
REVERT: N  526 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6895 (mp10)
  outliers start: 55
  outliers final: 21
  residues processed: 174
  average time/residue: 0.6345
  time to fit residues: 120.3659
Evaluate side-chains
  163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:   30.0000
   chunk 94 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  73 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.156935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119767 restraints weight = 17720.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.22
r_work: 0.3318 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.334  17435  Z= 0.153
  Angle     :  0.645  16.318  24838  Z= 0.344
  Chirality :  0.046   0.395   2783
  Planarity :  0.005   0.098   2169
  Dihedral  : 29.324 174.760   4716
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.11 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.24), residues: 1293
  helix:  2.33 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.46 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG N 185 
 TYR   0.011   0.001   TYR D  34 
 PHE   0.009   0.001   PHE N 503 
 TRP   0.011   0.001   TRP N 436 
 HIS   0.003   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 (17427)
  covalent geometry    : angle       0.63907 /  0.34 (24826)
  SS BOND              : bond        0.00781 /  0.38 (    3)
  SS BOND              : angle       0.49915 /  0.36 (    6)
  hydrogen bonds       : bond        0.05355 /  3.61 (  900)
  hydrogen bonds       : angle       3.33230 /  2.41 ( 2303)
  Misc. bond           : bond        0.19307 /  9.19 (    3)
  link_NAG-ASN         : bond        0.01261 /  0.84 (    2)
  link_NAG-ASN         : angle       5.81154 /  3.38 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7997 (tttt) cc_final: 0.7654 (tttm)
REVERT: A  129 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7876 (tmt170)
REVERT: C   15 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8148 (ptmm)
REVERT: D   32 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7312 (pt0)
REVERT: E   59 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8036 (pt0)
REVERT: E  131 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7397 (mtp85)
REVERT: G   74 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8331 (mtmm)
REVERT: G   92 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7564 (mm-30)
REVERT: G   95 LYS cc_start: 0.8774 (tttt) cc_final: 0.8537 (ttmt)
REVERT: G  108 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8675 (mp)
REVERT: H   30 ARG cc_start: 0.8014 (mmt90) cc_final: 0.6780 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8356 (mmt90)
REVERT: H   90 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: M   27 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8252 (mtp85)
REVERT: M   52 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7435 (mttp)
REVERT: N  210 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7167 (mp)
REVERT: N  249 MET cc_start: 0.8667 (mmm) cc_final: 0.8411 (mmt)
REVERT: N  526 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6923 (mp10)
REVERT: N  530 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8265 (mt0)
  outliers start: 38
  outliers final: 25
  residues processed: 162
  average time/residue: 0.6724
  time to fit residues: 119.1168
Evaluate side-chains
  169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 114 optimal weight:    0.3980
   chunk 104 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 152 optimal weight:    4.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.120211 restraints weight = 17693.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.23
r_work: 0.3326 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.341  17435  Z= 0.143
  Angle     :  0.636  15.869  24838  Z= 0.340
  Chirality :  0.046   0.384   2783
  Planarity :  0.004   0.102   2169
  Dihedral  : 29.315 174.264   4716
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.56 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.24), residues: 1293
  helix:  2.37 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.44 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG N 185 
 TYR   0.012   0.001   TYR D  34 
 PHE   0.009   0.001   PHE M  86 
 TRP   0.010   0.001   TRP N 436 
 HIS   0.002   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.14 (17427)
  covalent geometry    : angle       0.62977 /  0.34 (24826)
  SS BOND              : bond        0.00273 /  0.16 (    3)
  SS BOND              : angle       1.56691 /  0.91 (    6)
  hydrogen bonds       : bond        0.05225 /  3.53 (  900)
  hydrogen bonds       : angle       3.28513 /  2.39 ( 2303)
  Misc. bond           : bond        0.19685 /  9.37 (    3)
  link_NAG-ASN         : bond        0.01223 /  0.82 (    2)
  link_NAG-ASN         : angle       5.72868 /  3.31 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7983 (tttt) cc_final: 0.7605 (tttm)
REVERT: A  129 ARG cc_start: 0.8212 (ttt180) cc_final: 0.7869 (tmt170)
REVERT: C   15 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8173 (ptmm)
REVERT: D   32 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7300 (pt0)
REVERT: E   59 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8031 (pt0)
REVERT: E  131 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7368 (mtp85)
REVERT: G   74 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8338 (mtmm)
REVERT: G   92 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7558 (mm-30)
REVERT: G   95 LYS cc_start: 0.8793 (tttt) cc_final: 0.8540 (ttmt)
REVERT: G  108 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8657 (mp)
REVERT: H   30 ARG cc_start: 0.8017 (mmt90) cc_final: 0.6839 (mtp-110)
REVERT: H   54 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7299 (tmtm)
REVERT: H   83 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8348 (mmt90)
REVERT: H   90 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7816 (mp0)
REVERT: M   27 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8257 (mtp85)
REVERT: M   52 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7437 (mttp)
REVERT: N  210 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7195 (mp)
REVERT: N  229 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7342 (mmp-170)
REVERT: N  249 MET cc_start: 0.8672 (mmm) cc_final: 0.8426 (mmt)
REVERT: N  526 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.6940 (mp10)
REVERT: N  530 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8289 (mt0)
  outliers start: 39
  outliers final: 22
  residues processed: 158
  average time/residue: 0.7570
  time to fit residues: 130.6246
Evaluate side-chains
  166 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  229 ARG
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  545 THR
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 128 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 129 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  73 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.157744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.120625 restraints weight = 17708.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.22
r_work: 0.3330 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.340  17435  Z= 0.138
  Angle     :  0.629  15.602  24838  Z= 0.336
  Chirality :  0.046   0.387   2783
  Planarity :  0.004   0.096   2169
  Dihedral  : 29.310 174.216   4716
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.38 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.24), residues: 1293
  helix:  2.41 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.43 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N 185 
 TYR   0.011   0.001   TYR D  34 
 PHE   0.008   0.001   PHE M  86 
 TRP   0.010   0.001   TRP N 436 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.14 (17427)
  covalent geometry    : angle       0.62272 /  0.34 (24826)
  SS BOND              : bond        0.00310 /  0.18 (    3)
  SS BOND              : angle       0.39480 /  0.30 (    6)
  hydrogen bonds       : bond        0.05103 /  3.44 (  900)
  hydrogen bonds       : angle       3.27100 /  2.37 ( 2303)
  Misc. bond           : bond        0.19650 /  9.36 (    3)
  link_NAG-ASN         : bond        0.01238 /  0.83 (    2)
  link_NAG-ASN         : angle       5.63523 /  3.27 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7979 (tttt) cc_final: 0.7599 (tttm)
REVERT: A  120 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8815 (mtt)
REVERT: A  129 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7875 (tmt170)
REVERT: C   15 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8168 (ptmm)
REVERT: D   32 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7304 (pt0)
REVERT: E   59 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8040 (pt0)
REVERT: E   64 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8273 (mttm)
REVERT: E  131 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7363 (mtp85)
REVERT: G   74 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8327 (mtmm)
REVERT: G   92 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7551 (mm-30)
REVERT: G   95 LYS cc_start: 0.8786 (tttt) cc_final: 0.8539 (ttmt)
REVERT: G  108 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8680 (mp)
REVERT: H   30 ARG cc_start: 0.8008 (mmt90) cc_final: 0.6824 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8645 (mmt-90) cc_final: 0.8340 (mmt90)
REVERT: H   90 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: M   27 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8226 (mtp85)
REVERT: M   52 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7428 (mttp)
REVERT: N  210 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7161 (mp)
REVERT: N  249 MET cc_start: 0.8657 (mmm) cc_final: 0.8411 (mmt)
REVERT: N  526 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6930 (mp10)
REVERT: N  530 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8266 (mt0)
  outliers start: 41
  outliers final: 25
  residues processed: 164
  average time/residue: 0.7036
  time to fit residues: 126.2819
Evaluate side-chains
  171 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  400 ASP
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  545 THR
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 116 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  73 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119486 restraints weight = 17826.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.22
r_work: 0.3314 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.322  17435  Z= 0.179
  Angle     :  0.636  16.418  24838  Z= 0.341
  Chirality :  0.047   0.384   2783
  Planarity :  0.005   0.105   2169
  Dihedral  : 29.323 173.780   4716
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.20 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.23), residues: 1293
  helix:  2.32 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.51 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 185 
 TYR   0.012   0.001   TYR D  34 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.008   0.001   TRP N 436 
 HIS   0.003   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 (17427)
  covalent geometry    : angle       0.62991 /  0.34 (24826)
  SS BOND              : bond        0.00395 /  0.23 (    3)
  SS BOND              : angle       0.84148 /  0.54 (    6)
  hydrogen bonds       : bond        0.05391 /  3.64 (  900)
  hydrogen bonds       : angle       3.26459 /  2.37 ( 2303)
  Misc. bond           : bond        0.18587 /  8.85 (    3)
  link_NAG-ASN         : bond        0.01065 /  0.71 (    2)
  link_NAG-ASN         : angle       5.65039 /  3.26 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 135
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7963 (tttt) cc_final: 0.7596 (tttm)
REVERT: A  129 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7938 (tmt170)
REVERT: C   15 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8183 (ptmm)
REVERT: D   32 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7302 (pt0)
REVERT: E   59 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (pt0)
REVERT: E   64 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (mttm)
REVERT: E  131 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7377 (mtp85)
REVERT: G   74 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8331 (mtmm)
REVERT: G   92 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7556 (mm-30)
REVERT: G   95 LYS cc_start: 0.8791 (tttt) cc_final: 0.8546 (ttmt)
REVERT: G  108 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8663 (mp)
REVERT: H   30 ARG cc_start: 0.8033 (mmt90) cc_final: 0.6814 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8380 (mmt90)
REVERT: H   90 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7824 (mp0)
REVERT: M   27 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8208 (mtp85)
REVERT: M   52 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7466 (mttp)
REVERT: N  185 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7792 (ttp-110)
REVERT: N  210 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7207 (mp)
REVERT: N  249 MET cc_start: 0.8681 (mmm) cc_final: 0.8429 (mmt)
REVERT: N  526 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6964 (mp10)
REVERT: N  530 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8296 (mt0)
  outliers start: 44
  outliers final: 23
  residues processed: 163
  average time/residue: 0.7994
  time to fit residues: 141.9154
Evaluate side-chains
  165 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  545 THR
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 129 optimal weight:    0.2980
   chunk 112 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 150 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 117 optimal weight:   10.0000
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  73 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.157859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.120633 restraints weight = 17723.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.24
r_work: 0.3330 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.324  17435  Z= 0.137
  Angle     :  0.632  16.000  24838  Z= 0.338
  Chirality :  0.045   0.376   2783
  Planarity :  0.004   0.093   2169
  Dihedral  : 29.305 173.946   4714
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.74 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.24), residues: 1293
  helix:  2.43 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.47 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N 333 
 TYR   0.011   0.001   TYR D  34 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.010   0.001   TRP N 436 
 HIS   0.003   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.14 (17427)
  covalent geometry    : angle       0.62655 /  0.34 (24826)
  SS BOND              : bond        0.00211 /  0.13 (    3)
  SS BOND              : angle       0.69896 /  0.44 (    6)
  hydrogen bonds       : bond        0.05007 /  3.38 (  900)
  hydrogen bonds       : angle       3.24138 /  2.36 ( 2303)
  Misc. bond           : bond        0.18721 /  8.91 (    3)
  link_NAG-ASN         : bond        0.01141 /  0.76 (    2)
  link_NAG-ASN         : angle       5.51667 /  3.20 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7940 (tttt) cc_final: 0.7561 (tttm)
REVERT: A  129 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7881 (tmt170)
REVERT: C   15 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8161 (ptmm)
REVERT: D   32 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7286 (pt0)
REVERT: E   59 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8039 (pt0)
REVERT: E   64 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8296 (mttm)
REVERT: E  131 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7369 (mtp85)
REVERT: G   74 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8318 (mtmm)
REVERT: G   95 LYS cc_start: 0.8769 (tttt) cc_final: 0.8530 (ttmt)
REVERT: G  108 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: H   30 ARG cc_start: 0.8027 (mmt90) cc_final: 0.6790 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8362 (mmt90)
REVERT: H   90 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7750 (mp0)
REVERT: M   27 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8197 (mtp85)
REVERT: M   52 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7447 (mttp)
REVERT: N  185 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7764 (ttp-110)
REVERT: N  210 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7153 (mp)
REVERT: N  249 MET cc_start: 0.8660 (mmm) cc_final: 0.8420 (mmt)
REVERT: N  526 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6917 (mp10)
REVERT: N  530 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8280 (mt0)
  outliers start: 35
  outliers final: 22
  residues processed: 157
  average time/residue: 0.8247
  time to fit residues: 140.9719
Evaluate side-chains
  163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   30 VAL
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  545 THR
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 125 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 136 optimal weight:    6.9990
   chunk 129 optimal weight:    0.0020
   chunk 46 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   chunk 114 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.8928

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
E 125 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 = 0.157843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120751 restraints weight = 17772.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.21
r_work: 0.3334 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.338  17435  Z= 0.143
  Angle     :  0.630  15.546  24838  Z= 0.337
  Chirality :  0.046   0.374   2783
  Planarity :  0.004   0.097   2169
  Dihedral  : 29.295 173.504   4714
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.01 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.24), residues: 1293
  helix:  2.44 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.47 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N 307 
 TYR   0.011   0.001   TYR D  34 
 PHE   0.009   0.001   PHE M  86 
 TRP   0.009   0.001   TRP N 436 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.14 (17427)
  covalent geometry    : angle       0.62416 /  0.34 (24826)
  SS BOND              : bond        0.00283 /  0.17 (    3)
  SS BOND              : angle       0.69892 /  0.47 (    6)
  hydrogen bonds       : bond        0.05009 /  3.38 (  900)
  hydrogen bonds       : angle       3.21457 /  2.34 ( 2303)
  Misc. bond           : bond        0.19523 /  9.30 (    3)
  link_NAG-ASN         : bond        0.01083 /  0.72 (    2)
  link_NAG-ASN         : angle       5.48472 /  3.17 (    6)

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

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

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2586 Ramachandran restraints generated.
    1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7926 (tttt) cc_final: 0.7541 (tttm)
REVERT: A  129 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7867 (tmt170)
REVERT: C   15 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8158 (ptmm)
REVERT: D   32 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7305 (pt0)
REVERT: E   59 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8036 (pt0)
REVERT: E  131 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7343 (mtp85)
REVERT: F   92 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8017 (ttp80)
REVERT: G   74 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8328 (mtmm)
REVERT: G   95 LYS cc_start: 0.8778 (tttt) cc_final: 0.8537 (ttmt)
REVERT: G  108 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8648 (mp)
REVERT: H   30 ARG cc_start: 0.8025 (mmt90) cc_final: 0.6798 (mtp-110)
REVERT: H   83 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8343 (mmt90)
REVERT: H   90 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7809 (mp0)
REVERT: M   27 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8210 (mtp85)
REVERT: M   52 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7455 (mttp)
REVERT: N  185 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7768 (ttp-110)
REVERT: N  210 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7183 (mp)
REVERT: N  249 MET cc_start: 0.8663 (mmm) cc_final: 0.8418 (mmt)
REVERT: N  526 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6925 (mp10)
REVERT: N  530 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8295 (mt0)
  outliers start: 33
  outliers final: 21
  residues processed: 154
  average time/residue: 0.8290
  time to fit residues: 139.2522
Evaluate side-chains
  163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   11 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain M residue   52 LYS
Chi-restraints excluded: chain N residue  174 SER
Chi-restraints excluded: chain N residue  210 LEU
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  287 MET
Chi-restraints excluded: chain N residue  310 LEU
Chi-restraints excluded: chain N residue  314 ARG
Chi-restraints excluded: chain N residue  330 ASN
Chi-restraints excluded: chain N residue  333 ARG
Chi-restraints excluded: chain N residue  453 THR
Chi-restraints excluded: chain N residue  522 MET
Chi-restraints excluded: chain N residue  526 GLN
Chi-restraints excluded: chain N residue  530 GLN
Chi-restraints excluded: chain N residue  545 THR
Chi-restraints excluded: chain N residue  553 MET
Chi-restraints excluded: chain N residue  556 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 102 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:   10.0000
   chunk 138 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 91 optimal weight:    9.9990
   overall best weight:    1.5982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  73 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120493 restraints weight = 17756.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.22
r_work: 0.3330 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
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      :  0.004   0.335  17435  Z= 0.163
  Angle     :  0.629  16.351  24838  Z= 0.336
  Chirality :  0.046   0.382   2783
  Planarity :  0.004   0.098   2169
  Dihedral  : 29.245 172.794   4714
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.92 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.48 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.24), residues: 1293
  helix:  2.39 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.48 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N 307 
 TYR   0.011   0.001   TYR D  34 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.008   0.001   TRP M  89 
 HIS   0.003   0.001   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 (17427)
  covalent geometry    : angle       0.62381 /  0.33 (24826)
  SS BOND              : bond        0.00896 /  0.44 (    3)
  SS BOND              : angle       0.38503 /  0.31 (    6)
  hydrogen bonds       : bond        0.05089 /  3.44 (  900)
  hydrogen bonds       : angle       3.20648 /  2.34 ( 2303)
  Misc. bond           : bond        0.19369 /  9.22 (    3)
  link_NAG-ASN         : bond        0.01008 /  0.67 (    2)
  link_NAG-ASN         : angle       5.45150 /  3.15 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5420.54 seconds
wall clock time: 92 minutes 55.92 seconds (5575.92 seconds total)