Starting phenix.real_space_refine
on Sun Apr 27 13:52:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hn4_0246/04_2025/6hn4_0246.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    3595      2.51       5
     N     981      2.21       5
     O    1078      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5702
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1629
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 3989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3989
          Classifications: {'peptide': 498}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 466}
          Chain breaks: 4
    Chain: "F"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.23, per 1000 atoms: 0.74
  Number of scatterers: 5702
  At special positions: 0
  Unit cell: (100.88, 105.04, 102.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1078      8.00
     N     981      7.00
     C    3595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 647 " - pdb=" SG  CYS E 841 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 767 " - pdb=" SG  CYS E 776 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F   8 " - pdb=" SG  CYS F  26 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 126 " - pdb=" SG  CYS F 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 159 " - pdb=" SG  CYS F 182 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 169 " - pdb=" SG  CYS F 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 192 " - pdb=" SG  CYS F 201 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 196 " - pdb=" SG  CYS F 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 208 " - pdb=" SG  CYS F 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 212 " - pdb=" SG  CYS F 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 228 " - pdb=" SG  CYS F 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 241 " - pdb=" SG  CYS F 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 259 " - pdb=" SG  CYS F 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 266 " - pdb=" SG  CYS F 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 288 " - pdb=" SG  CYS F 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 304 " - pdb=" SG  CYS F 308 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 647 " - pdb=" SG  CYS F 841 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 767 " - pdb=" SG  CYS F 776 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG F1001 " - " ASN F  16 "
      " NAG F1002 " - " ASN F  25 "
      " NAG F1003 " - " ASN F 111 "
      " NAG F1004 " - " ASN F 606 "
      " NAG F1005 " - " ASN F 875 "
      " NAG F1006 " - " ASN F 215 "
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 920.0 milliseconds
  

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      8.9% alpha, 37.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'E' and resid 638 through 644
      removed outlier: 4.029A  pdb=" N   LEU E 644 " --> pdb=" O   LEU E 641 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 844 through 851
    Processing helix  chain 'F' and resid 17 through 24
    Processing helix  chain 'F' and resid 42 through 48
      removed outlier: 3.801A  pdb=" N   PHE F  46 " --> pdb=" O   ARG F  42 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP F  48 " --> pdb=" O   GLU F  44 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 132 through 136
    Processing helix  chain 'F' and resid 255 through 266
      removed outlier: 3.507A  pdb=" N   CYS F 259 " --> pdb=" O   ASN F 255 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 638 through 644
      removed outlier: 4.039A  pdb=" N   LEU F 644 " --> pdb=" O   LEU F 641 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 844 through 851
    Processing sheet with id=AA1, first strand: chain 'E' and resid 599 through 604
      removed outlier: 6.521A  pdb=" N   LYS E 614 " --> pdb=" O   PRO E 601 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   SER E 603 " --> pdb=" O   ILE E 612 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE E 612 " --> pdb=" O   SER E 603 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 740 through 743
    Processing sheet with id=AA3, first strand: chain 'E' and resid 800 through 803
    Processing sheet with id=AA4, first strand: chain 'E' and resid 841 through 843
      removed outlier: 3.660A  pdb=" N   ALA E 869 " --> pdb=" O   GLY E 876 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 841 through 843
    Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 14
      removed outlier: 6.557A  pdb=" N   GLU F   6 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU F  30 " --> pdb=" O   GLU F   6 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS F   8 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   HIS F  32 " --> pdb=" O   CYS F   8 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLY F  10 " --> pdb=" O   HIS F  32 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLN F  34 " --> pdb=" O   GLY F  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP F  12 " --> pdb=" O   GLN F  34 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU F  36 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG F  14 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET F  38 " --> pdb=" O   ARG F  14 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE F  82 " --> pdb=" O   ASN F 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 14
      removed outlier: 6.557A  pdb=" N   GLU F   6 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU F  30 " --> pdb=" O   GLU F   6 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS F   8 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   HIS F  32 " --> pdb=" O   CYS F   8 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLY F  10 " --> pdb=" O   HIS F  32 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLN F  34 " --> pdb=" O   GLY F  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP F  12 " --> pdb=" O   GLN F  34 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU F  36 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG F  14 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET F  38 " --> pdb=" O   ARG F  14 " (cutoff:3.500A)
      removed outlier: 9.006A  pdb=" N   LEU F  62 " --> pdb=" O   GLY F  31 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU F  33 " --> pdb=" O   LEU F  62 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   PHE F  64 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE F  35 " --> pdb=" O   PHE F  64 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL F  66 " --> pdb=" O   ILE F  35 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   LEU F  37 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU F  61 " --> pdb=" O   VAL F  94 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   PHE F  96 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU F  63 " --> pdb=" O   PHE F  96 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TYR F  91 " --> pdb=" O   SER F 116 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ARG F 118 " --> pdb=" O   TYR F  91 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU F  93 " --> pdb=" O   ARG F 118 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   GLU F 120 " --> pdb=" O   LEU F  93 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE F  95 " --> pdb=" O   GLU F 120 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL F 117 " --> pdb=" O   HIS F 144 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL F 146 " --> pdb=" O   VAL F 117 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE F 119 " --> pdb=" O   VAL F 146 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 171 through 173
    Processing sheet with id=AA9, first strand: chain 'F' and resid 231 through 233
    Processing sheet with id=AB1, first strand: chain 'F' and resid 252 through 254
      removed outlier: 6.728A  pdb=" N   HIS F 247 " --> pdb=" O   CYS F 284 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 292 through 295
      removed outlier: 3.516A  pdb=" N   LEU F 300 " --> pdb=" O   ASN F 295 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 599 through 604
      removed outlier: 6.540A  pdb=" N   LYS F 614 " --> pdb=" O   PRO F 601 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   SER F 603 " --> pdb=" O   ILE F 612 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE F 612 " --> pdb=" O   SER F 603 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 740 through 744
    Processing sheet with id=AB5, first strand: chain 'F' and resid 800 through 803
    Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 843
      removed outlier: 3.559A  pdb=" N   ALA F 869 " --> pdb=" O   GLY F 876 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 841 through 843

    167 hydrogen bonds defined for protein.
    387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.32

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1865
        1.35 -     1.48: 1492
        1.48 -     1.60: 2430
        1.60 -     1.73: 0
        1.73 -     1.86: 58
  Bond restraints: 5845
  Sorted by residual:
  bond pdb=" C   THR F 771 "
       pdb=" N   PRO F 772 "
    ideal  model  delta    sigma   weight residual
    1.334  1.427 -0.093 2.34e-02 1.83e+03 1.58e+01
  bond pdb=" CA  THR F 771 "
       pdb=" C   THR F 771 "
    ideal  model  delta    sigma   weight residual
    1.524  1.561 -0.037 1.26e-02 6.30e+03 8.83e+00
  bond pdb=" C1  NAG F1005 "
       pdb=" O5  NAG F1005 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.77e+00
  bond pdb=" C1  NAG F1004 "
       pdb=" O5  NAG F1004 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" N   ASN F  90 "
       pdb=" CA  ASN F  90 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.83e-02 2.99e+03 4.35e+00
  ... (remaining 5840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.00: 7817
        5.00 -     9.99: 110
        9.99 -    14.99: 6
       14.99 -    19.99: 0
       19.99 -    24.99: 2
  Bond angle restraints: 7935
  Sorted by residual:
  angle pdb=" C   LYS F 197 "
        pdb=" N   SER F 198 "
        pdb=" CA  SER F 198 "
      ideal   model   delta    sigma   weight residual
     122.06  109.66   12.40 1.86e+00 2.89e-01 4.45e+01
  angle pdb=" C   VAL F  99 "
        pdb=" N   HIS F 100 "
        pdb=" CA  HIS F 100 "
      ideal   model   delta    sigma   weight residual
     121.54  132.94  -11.40 1.91e+00 2.74e-01 3.56e+01
  angle pdb=" N   LYS F 197 "
        pdb=" CA  LYS F 197 "
        pdb=" C   LYS F 197 "
      ideal   model   delta    sigma   weight residual
     110.80  123.37  -12.57 2.13e+00 2.20e-01 3.48e+01
  angle pdb=" CA  GLU F 773 "
        pdb=" CB  GLU F 773 "
        pdb=" CG  GLU F 773 "
      ideal   model   delta    sigma   weight residual
     114.10  124.68  -10.58 2.00e+00 2.50e-01 2.80e+01
  angle pdb=" C   PRO E 816 "
        pdb=" N   LYS E 817 "
        pdb=" CA  LYS E 817 "
      ideal   model   delta    sigma   weight residual
     121.54  131.28   -9.74 1.91e+00 2.74e-01 2.60e+01
  ... (remaining 7930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 3405
       14.98 -    29.96: 183
       29.96 -    44.94: 41
       44.94 -    59.92: 7
       59.92 -    74.90: 3
  Dihedral angle restraints: 3639
    sinusoidal: 1591
      harmonic: 2048
  Sorted by residual:
  dihedral pdb=" CB  CYS E 647 "
           pdb=" SG  CYS E 647 "
           pdb=" SG  CYS E 841 "
           pdb=" CB  CYS E 841 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.92  -71.92     1      1.00e+01 1.00e-02 6.62e+01
  dihedral pdb=" C   THR F 771 "
           pdb=" N   THR F 771 "
           pdb=" CA  THR F 771 "
           pdb=" CB  THR F 771 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.47   13.47     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" SG  CYS F 304 "
           pdb=" CB  CYS F 308 "
           pdb=" SG  CYS F 308 "
           pdb=" CA  CYS F 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    4.10   74.90     1      2.00e+01 2.50e-03 1.77e+01
  ... (remaining 3636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 632
       0.075 -    0.149: 203
       0.149 -    0.224: 34
       0.224 -    0.299: 7
       0.299 -    0.373: 1
  Chirality restraints: 877
  Sorted by residual:
  chirality pdb=" CA  THR F 771 "
            pdb=" N   THR F 771 "
            pdb=" C   THR F 771 "
            pdb=" CB  THR F 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CB  VAL F 146 "
            pdb=" CA  VAL F 146 "
            pdb=" CG1 VAL F 146 "
            pdb=" CG2 VAL F 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  GLU F 773 "
            pdb=" N   GLU F 773 "
            pdb=" C   GLU F 773 "
            pdb=" CB  GLU F 773 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 874 not shown)

  Planarity restraints: 1030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F 818 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.78e+00
        pdb=" CD  GLU F 818 "    0.054 2.00e-02 2.50e+03
        pdb=" OE1 GLU F 818 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE2 GLU F 818 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 612 "   -0.015 2.00e-02 2.50e+03   3.11e-02 9.66e+00
        pdb=" C   ILE E 612 "    0.054 2.00e-02 2.50e+03
        pdb=" O   ILE E 612 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU E 613 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 612 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.33e+00
        pdb=" C   ILE F 612 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ILE F 612 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU F 613 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1027 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 327
        2.73 -     3.27: 5041
        3.27 -     3.81: 9021
        3.81 -     4.36: 10732
        4.36 -     4.90: 18402
  Nonbonded interactions: 43523
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 781 "
            pdb=" OH  TYR F  67 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER F 829 "
            pdb=" O   ARG F 866 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER E 829 "
            pdb=" O   ARG E 866 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NE2 GLN F 610 "
            pdb=" OG  SER F 752 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   SER E 859 "
            pdb=" OH  TYR E 863 "
     model   vdw
     2.368 3.040
  ... (remaining 43518 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.050
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.480
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093   5869  Z= 0.321
  Angle     :  1.515  24.985   7989  Z= 0.826
  Chirality :  0.075   0.373    877
  Planarity :  0.007   0.031   1024
  Dihedral  :  9.899  69.511   2259
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  1.75 %
    Allowed  :  6.87 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.30), residues: 684
  helix: -2.61 (0.76), residues: 28
  sheet: -1.98 (0.31), residues: 202
  loop : -1.09 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP F 878 
 HIS   0.021   0.002   HIS F  32 
 PHE   0.039   0.004   PHE F 231 
 TYR   0.021   0.004   TYR F  60 
 ARG   0.037   0.006   ARG F 866 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00590 (    6)
  link_NAG-ASN         : angle       2.47728 (   18)
  hydrogen bonds       : bond        0.14724 (  147)
  hydrogen bonds       : angle       9.25815 (  387)
  SS BOND              : bond        0.00838 (   18)
  SS BOND              : angle       3.50355 (   36)
  covalent geometry    : bond        0.00674 ( 5845)
  covalent geometry    : angle       1.49713 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  600 ASP cc_start: 0.8950 (m-30) cc_final: 0.8727 (t0)
REVERT: E  740 PHE cc_start: 0.9044 (p90) cc_final: 0.8685 (p90)
REVERT: E  741 GLU cc_start: 0.8475 (tp30) cc_final: 0.7661 (tm-30)
REVERT: E  747 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8524 (mt-10)
REVERT: E  749 LEU cc_start: 0.8725 (tp) cc_final: 0.8498 (tp)
REVERT: E  800 THR cc_start: 0.9157 (m) cc_final: 0.8753 (p)
REVERT: E  802 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9055 (pt0)
REVERT: E  812 MET cc_start: 0.9457 (mtm) cc_final: 0.9029 (mpp)
REVERT: E  815 GLU cc_start: 0.9146 (pt0) cc_final: 0.8808 (tm-30)
REVERT: E  826 TYR cc_start: 0.8569 (m-80) cc_final: 0.8270 (m-80)
REVERT: E  885 TYR cc_start: 0.9234 (t80) cc_final: 0.8973 (t80)
REVERT: F   94 VAL cc_start: 0.8799 (t) cc_final: 0.8573 (t)
REVERT: F  125 LEU cc_start: 0.9035 (tp) cc_final: 0.8686 (tp)
REVERT: F  131 ILE cc_start: 0.8005 (mt) cc_final: 0.7755 (mt)
REVERT: F  249 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8403 (tp40)
REVERT: F  600 ASP cc_start: 0.8310 (m-30) cc_final: 0.7677 (t0)
REVERT: F  629 LEU cc_start: 0.8973 (tp) cc_final: 0.8474 (mt)
REVERT: F  757 PHE cc_start: 0.8658 (t80) cc_final: 0.8358 (t80)
REVERT: F  787 MET cc_start: 0.8877 (mtt) cc_final: 0.8146 (mtp)
REVERT: F  812 MET cc_start: 0.9095 (mtm) cc_final: 0.8653 (mpp)
REVERT: F  830 TYR cc_start: 0.8242 (p90) cc_final: 0.7950 (p90)
REVERT: F  870 THR cc_start: 0.9273 (m) cc_final: 0.9057 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2238
  time to fit residues: 48.3464
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
E 610 GLN
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 GLN
F  15 ASN
F 123 ASN
F 187 HIS
F 209 HIS
F 610 GLN
F 814 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.076795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.062709 restraints weight = 27077.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.064643 restraints weight = 16544.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.066006 restraints weight = 11596.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5869  Z= 0.221
  Angle     :  0.806  13.193   7989  Z= 0.399
  Chirality :  0.048   0.241    877
  Planarity :  0.004   0.035   1024
  Dihedral  :  6.331  43.174    890
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.72 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.32), residues: 684
  helix: -0.62 (1.00), residues: 28
  sheet: -0.90 (0.34), residues: 194
  loop : -0.34 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 133 
 HIS   0.007   0.001   HIS F 185 
 PHE   0.013   0.002   PHE F  64 
 TYR   0.016   0.002   TYR E 628 
 ARG   0.006   0.001   ARG E 761 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    6)
  link_NAG-ASN         : angle       2.58037 (   18)
  hydrogen bonds       : bond        0.04649 (  147)
  hydrogen bonds       : angle       6.66566 (  387)
  SS BOND              : bond        0.00632 (   18)
  SS BOND              : angle       1.25898 (   36)
  covalent geometry    : bond        0.00492 ( 5845)
  covalent geometry    : angle       0.79514 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8855 (p90) cc_final: 0.8629 (p90)
REVERT: E  826 TYR cc_start: 0.8117 (m-80) cc_final: 0.7908 (m-80)
REVERT: F   38 MET cc_start: 0.8460 (mtt) cc_final: 0.7748 (mmm)
REVERT: F  125 LEU cc_start: 0.8519 (tp) cc_final: 0.8114 (tp)
REVERT: F  246 TYR cc_start: 0.8695 (m-80) cc_final: 0.8455 (m-80)
REVERT: F  641 LEU cc_start: 0.9014 (mp) cc_final: 0.8725 (mt)
REVERT: F  757 PHE cc_start: 0.8336 (t80) cc_final: 0.8019 (t80)
REVERT: F  787 MET cc_start: 0.9215 (mtt) cc_final: 0.8526 (mtp)
REVERT: F  823 ILE cc_start: 0.8231 (mm) cc_final: 0.7742 (mm)
REVERT: F  870 THR cc_start: 0.9310 (m) cc_final: 0.9094 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2509
  time to fit residues: 35.5379
Evaluate side-chains
  73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 52 optimal weight:    0.0070
   chunk 65 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
E 635 GLN
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 GLN
E 839 HIS
F 769 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.077682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.064398 restraints weight = 27335.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.066239 restraints weight = 17035.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.067540 restraints weight = 12050.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5869  Z= 0.124
  Angle     :  0.682   9.523   7989  Z= 0.340
  Chirality :  0.047   0.169    877
  Planarity :  0.004   0.033   1024
  Dihedral  :  5.973  41.874    890
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.35 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.32), residues: 684
  helix:  0.45 (1.10), residues: 28
  sheet: -0.43 (0.35), residues: 190
  loop : -0.14 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 632 
 HIS   0.006   0.001   HIS F 264 
 PHE   0.036   0.002   PHE E 757 
 TYR   0.011   0.001   TYR E 863 
 ARG   0.008   0.001   ARG E 831 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    6)
  link_NAG-ASN         : angle       2.12075 (   18)
  hydrogen bonds       : bond        0.03754 (  147)
  hydrogen bonds       : angle       6.22869 (  387)
  SS BOND              : bond        0.00363 (   18)
  SS BOND              : angle       1.03236 (   36)
  covalent geometry    : bond        0.00279 ( 5845)
  covalent geometry    : angle       0.67362 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  812 MET cc_start: 0.8744 (mpp) cc_final: 0.8475 (mpp)
REVERT: E  817 LYS cc_start: 0.8839 (pttp) cc_final: 0.8492 (tppt)
REVERT: F  125 LEU cc_start: 0.8286 (tp) cc_final: 0.7907 (tp)
REVERT: F  638 ASP cc_start: 0.8442 (m-30) cc_final: 0.8221 (t70)
REVERT: F  787 MET cc_start: 0.9250 (mtt) cc_final: 0.8691 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1814
  time to fit residues: 23.2596
Evaluate side-chains
  66 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
E 814 GLN
F 218 GLN
F 610 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.075491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.062388 restraints weight = 28577.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.064117 restraints weight = 18264.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.065324 restraints weight = 13064.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5869  Z= 0.164
  Angle     :  0.691   8.820   7989  Z= 0.345
  Chirality :  0.048   0.219    877
  Planarity :  0.004   0.034   1024
  Dihedral  :  5.664  35.747    890
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.98 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.33), residues: 684
  helix:  0.74 (1.02), residues: 28
  sheet: -0.15 (0.35), residues: 203
  loop : -0.06 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 133 
 HIS   0.004   0.001   HIS F 185 
 PHE   0.023   0.002   PHE E 757 
 TYR   0.011   0.001   TYR F  60 
 ARG   0.005   0.001   ARG E 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    6)
  link_NAG-ASN         : angle       2.34013 (   18)
  hydrogen bonds       : bond        0.03740 (  147)
  hydrogen bonds       : angle       5.92506 (  387)
  SS BOND              : bond        0.00313 (   18)
  SS BOND              : angle       1.08004 (   36)
  covalent geometry    : bond        0.00364 ( 5845)
  covalent geometry    : angle       0.68084 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8763 (p90) cc_final: 0.8484 (p90)
REVERT: F  125 LEU cc_start: 0.8259 (tp) cc_final: 0.7957 (tp)
REVERT: F  638 ASP cc_start: 0.8529 (m-30) cc_final: 0.8272 (t70)
REVERT: F  787 MET cc_start: 0.9296 (mtt) cc_final: 0.8665 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1924
  time to fit residues: 23.9210
Evaluate side-chains
  64 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 GLN
F 218 GLN
F 814 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.074537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.061453 restraints weight = 28260.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.063101 restraints weight = 18274.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.064259 restraints weight = 13268.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5869  Z= 0.152
  Angle     :  0.656   8.514   7989  Z= 0.331
  Chirality :  0.047   0.198    877
  Planarity :  0.004   0.028   1024
  Dihedral  :  5.271  33.232    890
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.57 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.33), residues: 684
  helix:  0.73 (0.95), residues: 34
  sheet:  0.09 (0.35), residues: 201
  loop : -0.03 (0.32), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 133 
 HIS   0.005   0.001   HIS F 839 
 PHE   0.017   0.001   PHE E 884 
 TYR   0.011   0.001   TYR F  60 
 ARG   0.005   0.001   ARG F  47 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    6)
  link_NAG-ASN         : angle       2.41996 (   18)
  hydrogen bonds       : bond        0.03570 (  147)
  hydrogen bonds       : angle       5.69308 (  387)
  SS BOND              : bond        0.00235 (   18)
  SS BOND              : angle       1.05290 (   36)
  covalent geometry    : bond        0.00344 ( 5845)
  covalent geometry    : angle       0.64382 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8802 (p90) cc_final: 0.8439 (p90)
REVERT: E  812 MET cc_start: 0.8825 (mpp) cc_final: 0.8456 (mpp)
REVERT: E  845 LYS cc_start: 0.9384 (tmmt) cc_final: 0.8834 (mtpt)
REVERT: F  125 LEU cc_start: 0.8122 (tp) cc_final: 0.7848 (tp)
REVERT: F  638 ASP cc_start: 0.8524 (m-30) cc_final: 0.8286 (t70)
  outliers start: 2
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1901
  time to fit residues: 21.5076
Evaluate side-chains
  65 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E 610 GLN
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 199 HIS
F 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.074948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.061890 restraints weight = 28359.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.063598 restraints weight = 18260.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.064743 restraints weight = 13206.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5869  Z= 0.122
  Angle     :  0.619   8.204   7989  Z= 0.312
  Chirality :  0.046   0.221    877
  Planarity :  0.004   0.028   1024
  Dihedral  :  4.958  29.332    890
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.33), residues: 684
  helix:  1.22 (0.98), residues: 34
  sheet:  0.22 (0.35), residues: 211
  loop :  0.02 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 133 
 HIS   0.011   0.001   HIS F 199 
 PHE   0.011   0.001   PHE E 757 
 TYR   0.017   0.001   TYR F 826 
 ARG   0.002   0.000   ARG F  47 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    6)
  link_NAG-ASN         : angle       2.21361 (   18)
  hydrogen bonds       : bond        0.03276 (  147)
  hydrogen bonds       : angle       5.47194 (  387)
  SS BOND              : bond        0.00294 (   18)
  SS BOND              : angle       1.03122 (   36)
  covalent geometry    : bond        0.00274 ( 5845)
  covalent geometry    : angle       0.60847 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8792 (p90) cc_final: 0.8393 (p90)
REVERT: E  845 LYS cc_start: 0.9375 (tmmt) cc_final: 0.8850 (mtpt)
REVERT: F   59 ASP cc_start: 0.7437 (m-30) cc_final: 0.7121 (m-30)
REVERT: F  125 LEU cc_start: 0.7925 (tp) cc_final: 0.7633 (tp)
REVERT: F  638 ASP cc_start: 0.8519 (m-30) cc_final: 0.8298 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1668
  time to fit residues: 17.8084
Evaluate side-chains
  65 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.2104

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

Flipped N/Q/H residues before XYZ refinement:
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.073946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.060944 restraints weight = 29151.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.062613 restraints weight = 18747.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.063769 restraints weight = 13558.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5869  Z= 0.147
  Angle     :  0.644  10.793   7989  Z= 0.320
  Chirality :  0.047   0.215    877
  Planarity :  0.004   0.027   1024
  Dihedral  :  4.922  25.395    890
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.33), residues: 684
  helix:  1.36 (0.99), residues: 34
  sheet:  0.37 (0.35), residues: 211
  loop :  0.01 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 133 
 HIS   0.004   0.001   HIS F 839 
 PHE   0.011   0.001   PHE F  64 
 TYR   0.018   0.001   TYR F 826 
 ARG   0.004   0.000   ARG E 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00180 (    6)
  link_NAG-ASN         : angle       2.34381 (   18)
  hydrogen bonds       : bond        0.03321 (  147)
  hydrogen bonds       : angle       5.38342 (  387)
  SS BOND              : bond        0.00299 (   18)
  SS BOND              : angle       1.00445 (   36)
  covalent geometry    : bond        0.00336 ( 5845)
  covalent geometry    : angle       0.63278 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  644 LEU cc_start: 0.8512 (mt) cc_final: 0.7996 (mt)
REVERT: E  812 MET cc_start: 0.8813 (mpp) cc_final: 0.8573 (mpp)
REVERT: E  845 LYS cc_start: 0.9357 (tmmt) cc_final: 0.8890 (mtpt)
REVERT: F   94 VAL cc_start: 0.9447 (t) cc_final: 0.9237 (p)
REVERT: F  125 LEU cc_start: 0.7926 (tp) cc_final: 0.7656 (tp)
REVERT: F  246 TYR cc_start: 0.8554 (m-80) cc_final: 0.7960 (m-80)
REVERT: F  638 ASP cc_start: 0.8668 (m-30) cc_final: 0.8402 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1695
  time to fit residues: 17.2937
Evaluate side-chains
  58 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0000
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 GLN
F  21 HIS
F 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.074712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.061755 restraints weight = 28192.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.063462 restraints weight = 18006.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.064663 restraints weight = 12920.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5869  Z= 0.110
  Angle     :  0.618   8.831   7989  Z= 0.306
  Chirality :  0.046   0.215    877
  Planarity :  0.003   0.027   1024
  Dihedral  :  4.702  20.201    890
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.47 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.34), residues: 684
  helix:  1.40 (0.99), residues: 34
  sheet:  0.48 (0.36), residues: 205
  loop :  0.02 (0.32), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 813 
 HIS   0.003   0.001   HIS F 846 
 PHE   0.014   0.001   PHE F  64 
 TYR   0.008   0.001   TYR F  60 
 ARG   0.014   0.000   ARG F 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    6)
  link_NAG-ASN         : angle       2.11270 (   18)
  hydrogen bonds       : bond        0.03142 (  147)
  hydrogen bonds       : angle       5.21032 (  387)
  SS BOND              : bond        0.00279 (   18)
  SS BOND              : angle       0.88434 (   36)
  covalent geometry    : bond        0.00251 ( 5845)
  covalent geometry    : angle       0.60944 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  644 LEU cc_start: 0.8520 (mt) cc_final: 0.8004 (mt)
REVERT: E  812 MET cc_start: 0.8865 (mpp) cc_final: 0.8621 (mpp)
REVERT: E  845 LYS cc_start: 0.9358 (tmmt) cc_final: 0.8942 (mtpt)
REVERT: F   94 VAL cc_start: 0.9446 (t) cc_final: 0.9241 (p)
REVERT: F  125 LEU cc_start: 0.7904 (tp) cc_final: 0.7626 (tp)
REVERT: F  246 TYR cc_start: 0.8526 (m-80) cc_final: 0.7945 (m-80)
REVERT: F  638 ASP cc_start: 0.8704 (m-30) cc_final: 0.8456 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1665
  time to fit residues: 17.8135
Evaluate side-chains
  58 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 22 optimal weight:    0.2980
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0870
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.075053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.062148 restraints weight = 28511.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.063958 restraints weight = 17732.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.065167 restraints weight = 12541.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.5885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5869  Z= 0.108
  Angle     :  0.620   8.600   7989  Z= 0.308
  Chirality :  0.046   0.213    877
  Planarity :  0.003   0.027   1024
  Dihedral  :  4.588  17.419    890
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.34), residues: 684
  helix:  0.57 (0.91), residues: 40
  sheet:  0.57 (0.36), residues: 205
  loop : -0.02 (0.33), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 813 
 HIS   0.003   0.001   HIS E 756 
 PHE   0.010   0.001   PHE F  64 
 TYR   0.008   0.001   TYR F  60 
 ARG   0.007   0.000   ARG F 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    6)
  link_NAG-ASN         : angle       2.05029 (   18)
  hydrogen bonds       : bond        0.03131 (  147)
  hydrogen bonds       : angle       5.08295 (  387)
  SS BOND              : bond        0.00272 (   18)
  SS BOND              : angle       0.84414 (   36)
  covalent geometry    : bond        0.00247 ( 5845)
  covalent geometry    : angle       0.61206 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  644 LEU cc_start: 0.8570 (mt) cc_final: 0.8055 (mt)
REVERT: E  812 MET cc_start: 0.8838 (mpp) cc_final: 0.8556 (mpp)
REVERT: E  845 LYS cc_start: 0.9381 (tmmt) cc_final: 0.9015 (mtpt)
REVERT: F  125 LEU cc_start: 0.7912 (tp) cc_final: 0.7600 (tp)
REVERT: F  246 TYR cc_start: 0.8503 (m-80) cc_final: 0.7971 (m-80)
REVERT: F  638 ASP cc_start: 0.8621 (m-30) cc_final: 0.8419 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1654
  time to fit residues: 17.4739
Evaluate side-chains
  59 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.074722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.061605 restraints weight = 29200.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.063398 restraints weight = 18315.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.064615 restraints weight = 13013.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5869  Z= 0.120
  Angle     :  0.635   9.129   7989  Z= 0.312
  Chirality :  0.047   0.216    877
  Planarity :  0.003   0.027   1024
  Dihedral  :  4.755  18.444    890
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.34), residues: 684
  helix:  0.65 (0.89), residues: 40
  sheet:  0.63 (0.36), residues: 201
  loop : -0.03 (0.33), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 813 
 HIS   0.003   0.001   HIS E 756 
 PHE   0.013   0.001   PHE F 884 
 TYR   0.018   0.001   TYR F 830 
 ARG   0.008   0.000   ARG F 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    6)
  link_NAG-ASN         : angle       2.58948 (   18)
  hydrogen bonds       : bond        0.03124 (  147)
  hydrogen bonds       : angle       5.08501 (  387)
  SS BOND              : bond        0.00273 (   18)
  SS BOND              : angle       0.83974 (   36)
  covalent geometry    : bond        0.00275 ( 5845)
  covalent geometry    : angle       0.62217 ( 7935)

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  644 LEU cc_start: 0.8605 (mt) cc_final: 0.8091 (mt)
REVERT: E  812 MET cc_start: 0.8829 (mpp) cc_final: 0.8512 (mpp)
REVERT: E  845 LYS cc_start: 0.9383 (tmmt) cc_final: 0.9014 (mtpt)
REVERT: F  246 TYR cc_start: 0.8524 (m-80) cc_final: 0.7970 (m-80)
REVERT: F  638 ASP cc_start: 0.8599 (m-30) cc_final: 0.8372 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1626
  time to fit residues: 16.9816
Evaluate side-chains
  56 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.074368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.061296 restraints weight = 28843.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.063041 restraints weight = 18606.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.064248 restraints weight = 13280.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.6069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5869  Z= 0.129
  Angle     :  0.629   8.000   7989  Z= 0.314
  Chirality :  0.047   0.215    877
  Planarity :  0.003   0.026   1024
  Dihedral  :  4.776  31.838    890
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.34), residues: 684
  helix:  0.55 (0.88), residues: 40
  sheet:  0.70 (0.36), residues: 201
  loop : -0.10 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 878 
 HIS   0.003   0.001   HIS E 756 
 PHE   0.013   0.001   PHE F 884 
 TYR   0.013   0.001   TYR F 127 
 ARG   0.007   0.000   ARG F 851 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    6)
  link_NAG-ASN         : angle       2.60532 (   18)
  hydrogen bonds       : bond        0.03171 (  147)
  hydrogen bonds       : angle       5.05211 (  387)
  SS BOND              : bond        0.00339 (   18)
  SS BOND              : angle       1.55779 (   36)
  covalent geometry    : bond        0.00298 ( 5845)
  covalent geometry    : angle       0.60985 ( 7935)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2270.47 seconds
wall clock time: 40 minutes 23.46 seconds (2423.46 seconds total)