Starting phenix.real_space_refine
on Tue Jul 29 23:35:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2025/7dsc_30830.cif"
  }
  resolution = 3.5
  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     104      5.16       5
     C    7736      2.51       5
     N    1888      2.21       5
     O    2120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11848
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1467
          Classifications: {'peptide': 191}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 181}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 5.49, per 1000 atoms: 0.46
  Number of scatterers: 11848
  At special positions: 0
  Unit cell: (124.722, 124.722, 88.218, 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     104     16.00
     O    2120      8.00
     N    1888      7.00
     C    7736      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  41 " - pdb=" SG  CYS G 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  41 " - pdb=" SG  CYS F 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  43 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  43 " - pdb=" SG  CYS E 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  43 " - pdb=" SG  CYS G 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  43 " - pdb=" SG  CYS F 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  43 " - pdb=" SG  CYS H 159 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1001 " - " ASN A 139 "
      " NAG B1001 " - " ASN B 139 "
      " NAG C1001 " - " ASN C 139 "
      " NAG D1001 " - " ASN D 139 "
      " NAG E1001 " - " ASN E 139 "
      " NAG F1001 " - " ASN F 139 "
      " NAG G1001 " - " ASN G 139 "
      " NAG H1001 " - " ASN H 139 "
  Time building additional restraints: 4.98
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2944

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      75.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 47 through 70
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 73 through 83
      removed outlier: 3.629A  pdb=" N   LEU A  77 " --> pdb=" O   ASN A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 107
    Processing helix  chain 'A' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
    Processing helix  chain 'A' and resid 146 through 156
      removed outlier: 4.037A  pdb=" N   LYS A 152 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 204
    Processing helix  chain 'B' and resid 6 through 18
    Processing helix  chain 'B' and resid 25 through 36
    Processing helix  chain 'B' and resid 47 through 70
      Proline residue:  B  59  - end of helix
    Processing helix  chain 'B' and resid 73 through 83
      removed outlier: 3.628A  pdb=" N   LEU B  77 " --> pdb=" O   ASN B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 107
    Processing helix  chain 'B' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA B 111 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
    Processing helix  chain 'B' and resid 146 through 156
      removed outlier: 4.036A  pdb=" N   LYS B 152 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE B 153 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 204
    Processing helix  chain 'C' and resid 6 through 18
    Processing helix  chain 'C' and resid 25 through 36
    Processing helix  chain 'C' and resid 47 through 70
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 73 through 83
      removed outlier: 3.629A  pdb=" N   LEU C  77 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 107
    Processing helix  chain 'C' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA C 111 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 129
    Processing helix  chain 'C' and resid 146 through 156
      removed outlier: 4.037A  pdb=" N   LYS C 152 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE C 153 " --> pdb=" O   GLU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 204
    Processing helix  chain 'D' and resid 6 through 18
    Processing helix  chain 'D' and resid 25 through 36
    Processing helix  chain 'D' and resid 47 through 70
      Proline residue:  D  59  - end of helix
    Processing helix  chain 'D' and resid 73 through 83
      removed outlier: 3.629A  pdb=" N   LEU D  77 " --> pdb=" O   ASN D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 107
    Processing helix  chain 'D' and resid 107 through 120
      removed outlier: 3.688A  pdb=" N   ALA D 111 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 129
    Processing helix  chain 'D' and resid 146 through 156
      removed outlier: 4.037A  pdb=" N   LYS D 152 " --> pdb=" O   LYS D 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE D 153 " --> pdb=" O   GLU D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 204
    Processing helix  chain 'E' and resid 6 through 18
    Processing helix  chain 'E' and resid 25 through 36
    Processing helix  chain 'E' and resid 47 through 70
      Proline residue:  E  59  - end of helix
    Processing helix  chain 'E' and resid 73 through 83
      removed outlier: 3.629A  pdb=" N   LEU E  77 " --> pdb=" O   ASN E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 107
    Processing helix  chain 'E' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA E 111 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 129
    Processing helix  chain 'E' and resid 146 through 156
      removed outlier: 4.037A  pdb=" N   LYS E 152 " --> pdb=" O   LYS E 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE E 153 " --> pdb=" O   GLU E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 204
    Processing helix  chain 'F' and resid 6 through 18
    Processing helix  chain 'F' and resid 25 through 36
    Processing helix  chain 'F' and resid 47 through 70
      Proline residue:  F  59  - end of helix
    Processing helix  chain 'F' and resid 73 through 83
      removed outlier: 3.628A  pdb=" N   LEU F  77 " --> pdb=" O   ASN F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 107
    Processing helix  chain 'F' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA F 111 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 129
    Processing helix  chain 'F' and resid 146 through 156
      removed outlier: 4.036A  pdb=" N   LYS F 152 " --> pdb=" O   LYS F 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE F 153 " --> pdb=" O   GLU F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 170 through 204
    Processing helix  chain 'G' and resid 6 through 18
    Processing helix  chain 'G' and resid 25 through 36
    Processing helix  chain 'G' and resid 47 through 70
      Proline residue:  G  59  - end of helix
    Processing helix  chain 'G' and resid 73 through 83
      removed outlier: 3.629A  pdb=" N   LEU G  77 " --> pdb=" O   ASN G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 107
    Processing helix  chain 'G' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA G 111 " --> pdb=" O   LEU G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 121 through 129
    Processing helix  chain 'G' and resid 146 through 156
      removed outlier: 4.037A  pdb=" N   LYS G 152 " --> pdb=" O   LYS G 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE G 153 " --> pdb=" O   GLU G 149 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 170 through 204
    Processing helix  chain 'H' and resid 6 through 18
    Processing helix  chain 'H' and resid 25 through 36
    Processing helix  chain 'H' and resid 47 through 70
      Proline residue:  H  59  - end of helix
    Processing helix  chain 'H' and resid 73 through 83
      removed outlier: 3.628A  pdb=" N   LEU H  77 " --> pdb=" O   ASN H  73 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 107
    Processing helix  chain 'H' and resid 107 through 120
      removed outlier: 3.689A  pdb=" N   ALA H 111 " --> pdb=" O   LEU H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 121 through 129
    Processing helix  chain 'H' and resid 146 through 156
      removed outlier: 4.036A  pdb=" N   LYS H 152 " --> pdb=" O   LYS H 148 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE H 153 " --> pdb=" O   GLU H 149 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 170 through 204

    809 hydrogen bonds defined for protein.
    2427 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: 3.54

  Time building geometry restraints manager: 5.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3624
        1.34 -     1.46: 2598
        1.46 -     1.58: 5738
        1.58 -     1.69: 0
        1.69 -     1.81: 160
  Bond restraints: 12120
  Sorted by residual:
  bond pdb=" C1  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG F1001 "
       pdb=" O5  NAG F1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG H1001 "
       pdb=" O5  NAG H1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG A1001 "
       pdb=" O5  NAG A1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.94e+00
  bond pdb=" C1  NAG C1001 "
       pdb=" O5  NAG C1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.94e+00
  ... (remaining 12115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 15639
        1.07 -     2.15: 674
        2.15 -     3.22: 95
        3.22 -     4.29: 24
        4.29 -     5.36: 40
  Bond angle restraints: 16472
  Sorted by residual:
  angle pdb=" N   VAL H  58 "
        pdb=" CA  VAL H  58 "
        pdb=" C   VAL H  58 "
      ideal   model   delta    sigma   weight residual
     108.88  113.31   -4.43 2.16e+00 2.14e-01 4.21e+00
  angle pdb=" N   VAL E  58 "
        pdb=" CA  VAL E  58 "
        pdb=" C   VAL E  58 "
      ideal   model   delta    sigma   weight residual
     108.88  113.27   -4.39 2.16e+00 2.14e-01 4.13e+00
  angle pdb=" N   VAL A  58 "
        pdb=" CA  VAL A  58 "
        pdb=" C   VAL A  58 "
      ideal   model   delta    sigma   weight residual
     108.88  113.27   -4.39 2.16e+00 2.14e-01 4.13e+00
  angle pdb=" N   VAL C  58 "
        pdb=" CA  VAL C  58 "
        pdb=" C   VAL C  58 "
      ideal   model   delta    sigma   weight residual
     108.88  113.27   -4.39 2.16e+00 2.14e-01 4.13e+00
  angle pdb=" N   VAL G  58 "
        pdb=" CA  VAL G  58 "
        pdb=" C   VAL G  58 "
      ideal   model   delta    sigma   weight residual
     108.88  113.27   -4.39 2.16e+00 2.14e-01 4.13e+00
  ... (remaining 16467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.98: 6520
       13.98 -    27.96: 560
       27.96 -    41.94: 200
       41.94 -    55.93: 64
       55.93 -    69.91: 8
  Dihedral angle restraints: 7352
    sinusoidal: 2840
      harmonic: 4512
  Sorted by residual:
  dihedral pdb=" CB  CYS H  43 "
           pdb=" SG  CYS H  43 "
           pdb=" SG  CYS H 159 "
           pdb=" CB  CYS H 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  119.88  -26.88     1      1.00e+01 1.00e-02 1.04e+01
  dihedral pdb=" CB  CYS F  43 "
           pdb=" SG  CYS F  43 "
           pdb=" SG  CYS F 159 "
           pdb=" CB  CYS F 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  119.87  -26.87     1      1.00e+01 1.00e-02 1.04e+01
  dihedral pdb=" CB  CYS B  43 "
           pdb=" SG  CYS B  43 "
           pdb=" SG  CYS B 159 "
           pdb=" CB  CYS B 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  119.87  -26.87     1      1.00e+01 1.00e-02 1.04e+01
  ... (remaining 7349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1284
       0.036 -    0.071: 501
       0.071 -    0.107: 116
       0.107 -    0.142: 27
       0.142 -    0.178: 8
  Chirality restraints: 1936
  Sorted by residual:
  chirality pdb=" CB  VAL D  58 "
            pdb=" CA  VAL D  58 "
            pdb=" CG1 VAL D  58 "
            pdb=" CG2 VAL D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CB  VAL B  58 "
            pdb=" CA  VAL B  58 "
            pdb=" CG1 VAL B  58 "
            pdb=" CG2 VAL B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.87e-01
  chirality pdb=" CB  VAL E  58 "
            pdb=" CA  VAL E  58 "
            pdb=" CG1 VAL E  58 "
            pdb=" CG2 VAL E  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 1933 not shown)

  Planarity restraints: 2032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO F  59 "   -0.031 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO F  60 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO F  60 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  60 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  59 "    0.031 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO B  60 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B  60 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  60 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  59 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO C  60 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2029 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3552
        2.82 -     3.34: 11795
        3.34 -     3.86: 19114
        3.86 -     4.38: 20138
        4.38 -     4.90: 36138
  Nonbonded interactions: 90737
  Sorted by model distance:
  nonbonded pdb=" OH  TYR G  68 "
            pdb=" OG1 THR G 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OH  TYR H  68 "
            pdb=" OG1 THR H 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OH  TYR A  68 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR E  68 "
            pdb=" OG1 THR E 103 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR C  68 "
            pdb=" OG1 THR C 103 "
     model   vdw
     2.300 3.040
  ... (remaining 90732 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: 0.14
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  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 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:             0.960
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     31.280
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.070
  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:3.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
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      :  0.004   0.039  12144  Z= 0.168
  Angle     :  0.577   5.363  16528  Z= 0.324
  Chirality :  0.040   0.178   1936
  Planarity :  0.004   0.046   2024
  Dihedral  : 12.770  69.908   4360
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.22 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.21), residues: 1480
  helix:  0.64 (0.15), residues: 1120
  sheet:  None (None), residues: 0
  loop : -2.98 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  62 
 HIS   0.001   0.000   HIS F 166 
 PHE   0.007   0.001   PHE D  64 
 TYR   0.008   0.001   TYR H 177 
 ARG   0.002   0.000   ARG F 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00430 (    8)
  link_NAG-ASN         : angle       3.34609 (   24)
  hydrogen bonds       : bond        0.13841 (  809)
  hydrogen bonds       : angle       4.96381 ( 2427)
  SS BOND              : bond        0.00189 (   16)
  SS BOND              : angle       0.84744 (   32)
  covalent geometry    : bond        0.00384 (12120)
  covalent geometry    : angle       0.56257 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  684 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 684
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8749 (mt) cc_final: 0.8504 (tp)
REVERT: A  134 LEU cc_start: 0.7989 (mt) cc_final: 0.7573 (mt)
REVERT: A  159 CYS cc_start: 0.4649 (m) cc_final: 0.4133 (m)
REVERT: B   26 MET cc_start: 0.7042 (mmm) cc_final: 0.6798 (mmm)
REVERT: B   95 LEU cc_start: 0.8719 (mt) cc_final: 0.8514 (tp)
REVERT: B  134 LEU cc_start: 0.7898 (mt) cc_final: 0.7489 (mt)
REVERT: B  185 CYS cc_start: 0.9068 (m) cc_final: 0.8527 (m)
REVERT: C   95 LEU cc_start: 0.8748 (mt) cc_final: 0.8503 (tp)
REVERT: C  134 LEU cc_start: 0.7986 (mt) cc_final: 0.7572 (mt)
REVERT: C  159 CYS cc_start: 0.4643 (m) cc_final: 0.4129 (m)
REVERT: D   26 MET cc_start: 0.7038 (mmm) cc_final: 0.6790 (mmm)
REVERT: D   95 LEU cc_start: 0.8718 (mt) cc_final: 0.8515 (tp)
REVERT: D  134 LEU cc_start: 0.7891 (mt) cc_final: 0.7481 (mt)
REVERT: D  185 CYS cc_start: 0.9068 (m) cc_final: 0.8525 (m)
REVERT: E   95 LEU cc_start: 0.8742 (mt) cc_final: 0.8497 (tp)
REVERT: E  134 LEU cc_start: 0.7989 (mt) cc_final: 0.7576 (mt)
REVERT: E  159 CYS cc_start: 0.4646 (m) cc_final: 0.4129 (m)
REVERT: F   26 MET cc_start: 0.7039 (mmm) cc_final: 0.6794 (mmm)
REVERT: F   95 LEU cc_start: 0.8721 (mt) cc_final: 0.8516 (tp)
REVERT: F  134 LEU cc_start: 0.7892 (mt) cc_final: 0.7485 (mt)
REVERT: F  185 CYS cc_start: 0.9068 (m) cc_final: 0.8532 (m)
REVERT: G   95 LEU cc_start: 0.8743 (mt) cc_final: 0.8497 (tp)
REVERT: G  134 LEU cc_start: 0.7993 (mt) cc_final: 0.7581 (mt)
REVERT: G  159 CYS cc_start: 0.4648 (m) cc_final: 0.4129 (m)
REVERT: H   26 MET cc_start: 0.7041 (mmm) cc_final: 0.6798 (mmm)
REVERT: H   95 LEU cc_start: 0.8722 (mt) cc_final: 0.8517 (tp)
REVERT: H  134 LEU cc_start: 0.7899 (mt) cc_final: 0.7489 (mt)
REVERT: H  185 CYS cc_start: 0.9065 (m) cc_final: 0.8529 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 684
  average time/residue: 0.3303
  time to fit residues: 316.6099
Evaluate side-chains
  510 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 510
  time to evaluate  : 2.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 115 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0370
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0670
   chunk 88 optimal weight:    2.9990
   chunk 138 optimal weight:    0.0170
   overall best weight:    0.3434

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.159829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.125967 restraints weight = 23022.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129263 restraints weight = 13607.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131389 restraints weight = 10051.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12144  Z= 0.149
  Angle     :  0.709   7.158  16528  Z= 0.359
  Chirality :  0.041   0.168   1936
  Planarity :  0.005   0.050   2024
  Dihedral  :  4.554  22.557   1792
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 25.91 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.23), residues: 1480
  helix:  1.82 (0.16), residues: 1112
  sheet:  None (None), residues: 0
  loop : -2.39 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  62 
 HIS   0.001   0.000   HIS G 166 
 PHE   0.022   0.002   PHE C  99 
 TYR   0.022   0.002   TYR B  51 
 ARG   0.007   0.001   ARG B 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    8)
  link_NAG-ASN         : angle       1.87737 (   24)
  hydrogen bonds       : bond        0.04209 (  809)
  hydrogen bonds       : angle       3.82768 ( 2427)
  SS BOND              : bond        0.00866 (   16)
  SS BOND              : angle       1.22844 (   32)
  covalent geometry    : bond        0.00315 (12120)
  covalent geometry    : angle       0.70490 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  624 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 581
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (t)
REVERT: B   71 ASN cc_start: 0.8455 (m-40) cc_final: 0.7462 (t0)
REVERT: B  170 SER cc_start: 0.8738 (t) cc_final: 0.8528 (t)
REVERT: B  185 CYS cc_start: 0.8797 (m) cc_final: 0.8275 (m)
REVERT: D  170 SER cc_start: 0.8755 (t) cc_final: 0.8540 (t)
REVERT: D  185 CYS cc_start: 0.8803 (m) cc_final: 0.8297 (m)
REVERT: F  170 SER cc_start: 0.8752 (t) cc_final: 0.8540 (t)
REVERT: F  185 CYS cc_start: 0.8822 (m) cc_final: 0.8310 (m)
REVERT: G  170 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8489 (t)
REVERT: H   71 ASN cc_start: 0.8448 (m-40) cc_final: 0.7649 (t0)
REVERT: H  170 SER cc_start: 0.8752 (t) cc_final: 0.8539 (t)
REVERT: H  185 CYS cc_start: 0.8821 (m) cc_final: 0.8301 (m)
  outliers start: 43
  outliers final: 24
  residues processed: 597
  average time/residue: 0.3222
  time to fit residues: 277.1254
Evaluate side-chains
  538 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 512
  time to evaluate  : 2.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue  161 ASP
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue  161 ASP
Chi-restraints excluded: chain G residue  170 SER
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 151 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 129 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** C  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.152005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.117438 restraints weight = 23128.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.120439 restraints weight = 13439.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.122571 restraints weight = 9940.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12144  Z= 0.163
  Angle     :  0.713   7.322  16528  Z= 0.358
  Chirality :  0.043   0.162   1936
  Planarity :  0.005   0.053   2024
  Dihedral  :  4.171  17.221   1792
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 25.91 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.22), residues: 1480
  helix:  1.91 (0.15), residues: 1120
  sheet:  None (None), residues: 0
  loop : -2.10 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  62 
 HIS   0.002   0.001   HIS G 166 
 PHE   0.025   0.002   PHE F  99 
 TYR   0.020   0.002   TYR D 142 
 ARG   0.002   0.000   ARG F 179 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00210 (    8)
  link_NAG-ASN         : angle       1.39790 (   24)
  hydrogen bonds       : bond        0.03913 (  809)
  hydrogen bonds       : angle       3.74417 ( 2427)
  SS BOND              : bond        0.00200 (   16)
  SS BOND              : angle       1.39684 (   32)
  covalent geometry    : bond        0.00394 (12120)
  covalent geometry    : angle       0.70964 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  543 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 484
  time to evaluate  : 1.216 
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: A   26 MET cc_start: 0.7010 (mmm) cc_final: 0.6709 (mmm)
REVERT: A   68 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6740 (m-80)
REVERT: A  170 SER cc_start: 0.8892 (t) cc_final: 0.8491 (m)
REVERT: B   71 ASN cc_start: 0.8329 (m-40) cc_final: 0.7861 (t0)
REVERT: B  170 SER cc_start: 0.8906 (t) cc_final: 0.8402 (m)
REVERT: B  185 CYS cc_start: 0.8750 (m) cc_final: 0.8278 (m)
REVERT: C   26 MET cc_start: 0.7010 (mmm) cc_final: 0.6708 (mmm)
REVERT: C   68 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6744 (m-80)
REVERT: D  170 SER cc_start: 0.8916 (t) cc_final: 0.8407 (m)
REVERT: D  185 CYS cc_start: 0.8758 (m) cc_final: 0.8285 (m)
REVERT: E   26 MET cc_start: 0.7021 (mmm) cc_final: 0.6716 (mmm)
REVERT: E   68 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6739 (m-80)
REVERT: F  165 GLU cc_start: 0.7197 (mp0) cc_final: 0.6997 (mp0)
REVERT: F  170 SER cc_start: 0.8907 (t) cc_final: 0.8399 (m)
REVERT: F  185 CYS cc_start: 0.8761 (m) cc_final: 0.8296 (m)
REVERT: G   26 MET cc_start: 0.7017 (mmm) cc_final: 0.6713 (mmm)
REVERT: G   68 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6736 (m-80)
REVERT: G  170 SER cc_start: 0.8877 (t) cc_final: 0.8477 (m)
REVERT: H   71 ASN cc_start: 0.8200 (m-40) cc_final: 0.7803 (t0)
REVERT: H  165 GLU cc_start: 0.7189 (mp0) cc_final: 0.6988 (mp0)
REVERT: H  170 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8398 (m)
REVERT: H  185 CYS cc_start: 0.8751 (m) cc_final: 0.8282 (m)
  outliers start: 59
  outliers final: 52
  residues processed: 513
  average time/residue: 0.2107
  time to fit residues: 156.8737
Evaluate side-chains
  528 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 471
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  157 ILE
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  180 CYS
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  153 ILE
Chi-restraints excluded: chain E residue  180 CYS
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  146 SER
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain F residue  169 ILE
Chi-restraints excluded: chain F residue  180 CYS
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  153 ILE
Chi-restraints excluded: chain G residue  180 CYS
Chi-restraints excluded: chain G residue  194 THR
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  161 ASP
Chi-restraints excluded: chain H residue  169 ILE
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain H residue  180 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 133 optimal weight:   40.0000
   chunk 52 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 115 optimal weight:    8.9990
   chunk 93 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.116001 restraints weight = 23304.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.119104 restraints weight = 13669.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.121080 restraints weight = 10124.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12144  Z= 0.164
  Angle     :  0.704   9.757  16528  Z= 0.351
  Chirality :  0.043   0.165   1936
  Planarity :  0.005   0.055   2024
  Dihedral  :  4.156  17.369   1792
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 27.40 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.22), residues: 1480
  helix:  1.98 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -2.23 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  62 
 HIS   0.001   0.000   HIS A 166 
 PHE   0.024   0.001   PHE D  99 
 TYR   0.019   0.002   TYR E 142 
 ARG   0.006   0.001   ARG A 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    8)
  link_NAG-ASN         : angle       1.64087 (   24)
  hydrogen bonds       : bond        0.03651 (  809)
  hydrogen bonds       : angle       3.75823 ( 2427)
  SS BOND              : bond        0.00055 (   16)
  SS BOND              : angle       0.92291 (   32)
  covalent geometry    : bond        0.00396 (12120)
  covalent geometry    : angle       0.70163 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  570 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 502
  time to evaluate  : 1.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.7104 (mmm) cc_final: 0.6735 (mmm)
REVERT: A   68 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6610 (m-80)
REVERT: A  140 GLU cc_start: 0.6544 (pm20) cc_final: 0.6036 (pm20)
REVERT: A  142 TYR cc_start: 0.6822 (m-80) cc_final: 0.6562 (m-80)
REVERT: A  156 LYS cc_start: 0.8052 (mttt) cc_final: 0.7791 (mtpt)
REVERT: A  160 LYS cc_start: 0.7472 (tppt) cc_final: 0.7082 (tppt)
REVERT: A  170 SER cc_start: 0.8902 (t) cc_final: 0.8532 (m)
REVERT: B   71 ASN cc_start: 0.8163 (m-40) cc_final: 0.7590 (t0)
REVERT: B  170 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8426 (m)
REVERT: B  185 CYS cc_start: 0.8697 (m) cc_final: 0.8311 (m)
REVERT: C   26 MET cc_start: 0.7086 (mmm) cc_final: 0.6485 (mmm)
REVERT: C   68 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6616 (m-80)
REVERT: C  140 GLU cc_start: 0.6546 (pm20) cc_final: 0.6060 (pm20)
REVERT: C  142 TYR cc_start: 0.6822 (m-80) cc_final: 0.6571 (m-80)
REVERT: C  156 LYS cc_start: 0.8054 (mttt) cc_final: 0.7790 (mtpt)
REVERT: C  160 LYS cc_start: 0.7465 (tppt) cc_final: 0.7086 (tppt)
REVERT: D  170 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8422 (m)
REVERT: D  185 CYS cc_start: 0.8713 (m) cc_final: 0.8330 (m)
REVERT: E   26 MET cc_start: 0.7086 (mmm) cc_final: 0.6490 (mmm)
REVERT: E   68 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6623 (m-80)
REVERT: E  140 GLU cc_start: 0.6531 (pm20) cc_final: 0.6045 (pm20)
REVERT: E  142 TYR cc_start: 0.6796 (m-80) cc_final: 0.6545 (m-80)
REVERT: E  156 LYS cc_start: 0.8053 (mttt) cc_final: 0.7789 (mtpt)
REVERT: E  160 LYS cc_start: 0.7470 (tppt) cc_final: 0.7088 (tppt)
REVERT: F  170 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8416 (m)
REVERT: F  185 CYS cc_start: 0.8704 (m) cc_final: 0.8320 (m)
REVERT: G   26 MET cc_start: 0.7095 (mmm) cc_final: 0.6722 (mmm)
REVERT: G   68 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6618 (m-80)
REVERT: G  140 GLU cc_start: 0.6533 (pm20) cc_final: 0.6026 (pm20)
REVERT: G  142 TYR cc_start: 0.6787 (m-80) cc_final: 0.6527 (m-80)
REVERT: G  156 LYS cc_start: 0.8049 (mttt) cc_final: 0.7796 (mtpt)
REVERT: G  160 LYS cc_start: 0.7474 (tppt) cc_final: 0.7083 (tppt)
REVERT: G  170 SER cc_start: 0.8883 (t) cc_final: 0.8512 (m)
REVERT: H   71 ASN cc_start: 0.8194 (m-40) cc_final: 0.7936 (t0)
REVERT: H  170 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8414 (m)
REVERT: H  185 CYS cc_start: 0.8703 (m) cc_final: 0.8317 (m)
  outliers start: 68
  outliers final: 52
  residues processed: 535
  average time/residue: 0.2772
  time to fit residues: 214.7331
Evaluate side-chains
  540 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 480
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  180 CYS
Chi-restraints excluded: chain B residue  194 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  157 ILE
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  170 SER
Chi-restraints excluded: chain D residue  180 CYS
Chi-restraints excluded: chain D residue  194 THR
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  180 CYS
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   56 LEU
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  146 SER
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain F residue  170 SER
Chi-restraints excluded: chain F residue  180 CYS
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  180 CYS
Chi-restraints excluded: chain G residue  194 THR
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  161 ASP
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain H residue  180 CYS
Chi-restraints excluded: chain H residue  194 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 68 optimal weight:    0.0270
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:   50.0000
   chunk 14 optimal weight:    0.0050
   chunk 82 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8056

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
C 104 GLN
E 104 GLN
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.152709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118710 restraints weight = 23264.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.121654 restraints weight = 13615.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.123761 restraints weight = 10084.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12144  Z= 0.140
  Angle     :  0.738  13.834  16528  Z= 0.357
  Chirality :  0.043   0.165   1936
  Planarity :  0.005   0.056   2024
  Dihedral  :  4.051  17.496   1792
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 27.40 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.22), residues: 1480
  helix:  2.11 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -1.96 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  62 
 HIS   0.001   0.001   HIS E 166 
 PHE   0.015   0.001   PHE D  99 
 TYR   0.012   0.001   TYR H 177 
 ARG   0.004   0.000   ARG G  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    8)
  link_NAG-ASN         : angle       1.86097 (   24)
  hydrogen bonds       : bond        0.03549 (  809)
  hydrogen bonds       : angle       3.68114 ( 2427)
  SS BOND              : bond        0.00078 (   16)
  SS BOND              : angle       0.61476 (   32)
  covalent geometry    : bond        0.00329 (12120)
  covalent geometry    : angle       0.73566 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  560 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 509
  time to evaluate  : 1.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.6953 (mmm) cc_final: 0.6290 (mmm)
REVERT: A   68 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6573 (m-80)
REVERT: A  103 THR cc_start: 0.8771 (m) cc_final: 0.8475 (p)
REVERT: A  104 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6376 (mp-120)
REVERT: A  160 LYS cc_start: 0.7542 (tppt) cc_final: 0.7198 (tppt)
REVERT: B   68 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6397 (m-80)
REVERT: B  170 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8812 (t)
REVERT: B  185 CYS cc_start: 0.8707 (m) cc_final: 0.8326 (m)
REVERT: C   26 MET cc_start: 0.6940 (mmm) cc_final: 0.6279 (mmm)
REVERT: C   68 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6562 (m-80)
REVERT: C  103 THR cc_start: 0.8775 (m) cc_final: 0.8482 (p)
REVERT: C  104 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6385 (mp-120)
REVERT: C  160 LYS cc_start: 0.7538 (tppt) cc_final: 0.7184 (tppt)
REVERT: D   68 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6352 (m-80)
REVERT: D  102 MET cc_start: 0.8570 (tpp) cc_final: 0.8368 (tpp)
REVERT: D  170 SER cc_start: 0.8954 (t) cc_final: 0.8424 (m)
REVERT: D  185 CYS cc_start: 0.8726 (m) cc_final: 0.8343 (m)
REVERT: E   26 MET cc_start: 0.6940 (mmm) cc_final: 0.6276 (mmm)
REVERT: E   68 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6555 (m-80)
REVERT: E  103 THR cc_start: 0.8777 (m) cc_final: 0.8484 (p)
REVERT: E  104 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6382 (mp-120)
REVERT: E  160 LYS cc_start: 0.7540 (tppt) cc_final: 0.7182 (tppt)
REVERT: F   68 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6371 (m-80)
REVERT: F  170 SER cc_start: 0.8941 (t) cc_final: 0.8415 (m)
REVERT: F  185 CYS cc_start: 0.8705 (m) cc_final: 0.8324 (m)
REVERT: G   26 MET cc_start: 0.6945 (mmm) cc_final: 0.6283 (mmm)
REVERT: G   68 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6579 (m-80)
REVERT: G  103 THR cc_start: 0.8774 (m) cc_final: 0.8480 (p)
REVERT: G  104 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6376 (mp-120)
REVERT: G  160 LYS cc_start: 0.7543 (tppt) cc_final: 0.7194 (tppt)
REVERT: H   71 ASN cc_start: 0.8136 (m-40) cc_final: 0.7684 (t0)
REVERT: H  102 MET cc_start: 0.8471 (tpp) cc_final: 0.8149 (tpp)
REVERT: H  170 SER cc_start: 0.8931 (t) cc_final: 0.8405 (m)
REVERT: H  185 CYS cc_start: 0.8699 (m) cc_final: 0.8336 (m)
  outliers start: 51
  outliers final: 32
  residues processed: 540
  average time/residue: 0.3073
  time to fit residues: 244.3099
Evaluate side-chains
  532 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 488
  time to evaluate  : 1.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  104 GLN
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  161 ASP
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  146 SER
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  104 GLN
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  161 ASP
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   66 LEU
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 134 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 127 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0000
   chunk 35 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 77 optimal weight:   30.0000
   chunk 2 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 102 optimal weight:    0.4980
   overall best weight:    0.8188

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

Flipped N/Q/H residues before XYZ refinement:
** D  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.118285 restraints weight = 23345.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.121403 restraints weight = 13526.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.123433 restraints weight = 9941.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12144  Z= 0.144
  Angle     :  0.758  14.033  16528  Z= 0.365
  Chirality :  0.043   0.181   1936
  Planarity :  0.005   0.057   2024
  Dihedral  :  4.084  17.813   1792
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 27.81 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.22), residues: 1480
  helix:  2.16 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -1.76 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  62 
 HIS   0.000   0.000   HIS H 166 
 PHE   0.025   0.001   PHE H  99 
 TYR   0.013   0.001   TYR A 142 
 ARG   0.003   0.000   ARG A  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    8)
  link_NAG-ASN         : angle       2.01235 (   24)
  hydrogen bonds       : bond        0.03526 (  809)
  hydrogen bonds       : angle       3.66267 ( 2427)
  SS BOND              : bond        0.00091 (   16)
  SS BOND              : angle       0.66776 (   32)
  covalent geometry    : bond        0.00336 (12120)
  covalent geometry    : angle       0.75462 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  562 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 514
  time to evaluate  : 2.883 
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: A   68 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6541 (m-80)
REVERT: A  140 GLU cc_start: 0.6575 (pm20) cc_final: 0.6037 (pm20)
REVERT: A  156 LYS cc_start: 0.8056 (mttt) cc_final: 0.7827 (mtpt)
REVERT: A  160 LYS cc_start: 0.7505 (tppt) cc_final: 0.7189 (tppt)
REVERT: B   32 GLN cc_start: 0.8551 (tp40) cc_final: 0.7628 (tm-30)
REVERT: B   68 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6442 (m-80)
REVERT: B  170 SER cc_start: 0.8980 (t) cc_final: 0.8435 (m)
REVERT: B  185 CYS cc_start: 0.8725 (m) cc_final: 0.8408 (m)
REVERT: C   68 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6540 (m-80)
REVERT: C  140 GLU cc_start: 0.6562 (pm20) cc_final: 0.6028 (pm20)
REVERT: C  156 LYS cc_start: 0.8056 (mttt) cc_final: 0.7826 (mtpt)
REVERT: C  160 LYS cc_start: 0.7500 (tppt) cc_final: 0.7195 (tppt)
REVERT: D   68 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6435 (m-80)
REVERT: D  102 MET cc_start: 0.8648 (tpp) cc_final: 0.8275 (tpp)
REVERT: D  170 SER cc_start: 0.8992 (t) cc_final: 0.8441 (m)
REVERT: D  185 CYS cc_start: 0.8751 (m) cc_final: 0.8439 (m)
REVERT: E   68 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6545 (m-80)
REVERT: E   92 PRO cc_start: 0.7653 (Cg_exo) cc_final: 0.7443 (Cg_endo)
REVERT: E  140 GLU cc_start: 0.6563 (pm20) cc_final: 0.6034 (pm20)
REVERT: E  156 LYS cc_start: 0.8053 (mttt) cc_final: 0.7829 (mtpt)
REVERT: E  160 LYS cc_start: 0.7497 (tppt) cc_final: 0.7188 (tppt)
REVERT: F   68 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6445 (m-80)
REVERT: F  170 SER cc_start: 0.8976 (t) cc_final: 0.8426 (m)
REVERT: F  185 CYS cc_start: 0.8730 (m) cc_final: 0.8424 (m)
REVERT: G   68 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6544 (m-80)
REVERT: G   92 PRO cc_start: 0.7628 (Cg_exo) cc_final: 0.7418 (Cg_endo)
REVERT: G  140 GLU cc_start: 0.6555 (pm20) cc_final: 0.6025 (pm20)
REVERT: G  156 LYS cc_start: 0.8049 (mttt) cc_final: 0.7824 (mtpt)
REVERT: G  160 LYS cc_start: 0.7504 (tppt) cc_final: 0.7197 (tppt)
REVERT: H   68 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6394 (m-80)
REVERT: H   71 ASN cc_start: 0.8181 (m-40) cc_final: 0.7597 (t0)
REVERT: H  102 MET cc_start: 0.8485 (tpp) cc_final: 0.8229 (tpp)
REVERT: H  170 SER cc_start: 0.8969 (t) cc_final: 0.8415 (m)
REVERT: H  185 CYS cc_start: 0.8691 (m) cc_final: 0.8392 (m)
  outliers start: 48
  outliers final: 38
  residues processed: 547
  average time/residue: 0.2638
  time to fit residues: 211.2072
Evaluate side-chains
  549 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 503
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  161 ASP
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  146 SER
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  161 ASP
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   66 LEU
Chi-restraints excluded: chain H residue   68 TYR
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  146 SER
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    3.9990
   chunk 139 optimal weight:    7.9990
   chunk 33 optimal weight:    0.2980
   chunk 71 optimal weight:    0.0970
   chunk 114 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0010
   chunk 116 optimal weight:    6.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 GLN
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.152764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118563 restraints weight = 23394.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.121658 restraints weight = 13653.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.123832 restraints weight = 10047.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12144  Z= 0.135
  Angle     :  0.776  14.481  16528  Z= 0.370
  Chirality :  0.042   0.165   1936
  Planarity :  0.005   0.058   2024
  Dihedral  :  3.996  22.365   1792
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 29.80 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.22), residues: 1480
  helix:  2.29 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -2.03 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  62 
 HIS   0.001   0.000   HIS C 166 
 PHE   0.022   0.001   PHE F  99 
 TYR   0.014   0.001   TYR B 177 
 ARG   0.004   0.000   ARG G  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00305 (    8)
  link_NAG-ASN         : angle       2.19307 (   24)
  hydrogen bonds       : bond        0.03435 (  809)
  hydrogen bonds       : angle       3.66865 ( 2427)
  SS BOND              : bond        0.00154 (   16)
  SS BOND              : angle       1.66997 (   32)
  covalent geometry    : bond        0.00310 (12120)
  covalent geometry    : angle       0.76973 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  539 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 498
  time to evaluate  : 1.372 
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: A   68 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6727 (m-80)
REVERT: A  160 LYS cc_start: 0.7582 (tppt) cc_final: 0.7358 (tppt)
REVERT: B   32 GLN cc_start: 0.8536 (tp40) cc_final: 0.7646 (tm-30)
REVERT: B   68 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6347 (m-80)
REVERT: B  170 SER cc_start: 0.8996 (t) cc_final: 0.8428 (m)
REVERT: B  185 CYS cc_start: 0.8692 (m) cc_final: 0.8477 (t)
REVERT: C   68 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6715 (m-80)
REVERT: C  160 LYS cc_start: 0.7578 (tppt) cc_final: 0.7350 (tppt)
REVERT: D   68 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6476 (m-80)
REVERT: D  102 MET cc_start: 0.8680 (tpp) cc_final: 0.8410 (tpp)
REVERT: D  170 SER cc_start: 0.8962 (t) cc_final: 0.8737 (t)
REVERT: D  185 CYS cc_start: 0.8705 (m) cc_final: 0.8155 (m)
REVERT: E   68 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6702 (m-80)
REVERT: E  160 LYS cc_start: 0.7579 (tppt) cc_final: 0.7347 (tppt)
REVERT: F   68 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6443 (m-80)
REVERT: F  170 SER cc_start: 0.8975 (t) cc_final: 0.8741 (t)
REVERT: F  185 CYS cc_start: 0.8703 (m) cc_final: 0.8153 (m)
REVERT: G   68 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6731 (m-80)
REVERT: G  160 LYS cc_start: 0.7578 (tppt) cc_final: 0.7353 (tppt)
REVERT: H   32 GLN cc_start: 0.8520 (tp40) cc_final: 0.7629 (tm-30)
REVERT: H   68 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6440 (m-80)
REVERT: H   71 ASN cc_start: 0.8205 (m-40) cc_final: 0.7444 (t0)
REVERT: H  102 MET cc_start: 0.8511 (tpp) cc_final: 0.8300 (tpp)
REVERT: H  170 SER cc_start: 0.8952 (t) cc_final: 0.8713 (t)
REVERT: H  185 CYS cc_start: 0.8667 (m) cc_final: 0.8457 (t)
  outliers start: 41
  outliers final: 26
  residues processed: 526
  average time/residue: 0.2214
  time to fit residues: 171.3043
Evaluate side-chains
  517 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 483
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   68 TYR
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 143 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 129 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 GLN
C 104 GLN
D 104 GLN
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 104 GLN
H 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.153249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119172 restraints weight = 23265.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.122283 restraints weight = 13819.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.124256 restraints weight = 10257.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12144  Z= 0.145
  Angle     :  0.861  14.869  16528  Z= 0.397
  Chirality :  0.045   0.181   1936
  Planarity :  0.005   0.058   2024
  Dihedral  :  4.003  27.613   1792
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 29.64 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.22), residues: 1480
  helix:  2.27 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -2.03 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP F  62 
 HIS   0.001   0.000   HIS C 166 
 PHE   0.033   0.001   PHE H  99 
 TYR   0.020   0.001   TYR D  51 
 ARG   0.004   0.000   ARG D 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    8)
  link_NAG-ASN         : angle       2.27145 (   24)
  hydrogen bonds       : bond        0.03446 (  809)
  hydrogen bonds       : angle       3.79246 ( 2427)
  SS BOND              : bond        0.00184 (   16)
  SS BOND              : angle       1.27597 (   32)
  covalent geometry    : bond        0.00341 (12120)
  covalent geometry    : angle       0.85671 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  534 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 484
  time to evaluate  : 1.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6607 (m-80)
REVERT: A  104 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7466 (mp10)
REVERT: B   68 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6398 (m-80)
REVERT: B  170 SER cc_start: 0.8977 (t) cc_final: 0.8769 (t)
REVERT: C   68 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6604 (m-80)
REVERT: D   68 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6441 (m-80)
REVERT: D  102 MET cc_start: 0.8591 (tpp) cc_final: 0.8359 (tpp)
REVERT: D  170 SER cc_start: 0.8939 (t) cc_final: 0.8706 (t)
REVERT: E   68 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6601 (m-80)
REVERT: E  104 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7465 (mp10)
REVERT: F   68 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6399 (m-80)
REVERT: F  170 SER cc_start: 0.8957 (t) cc_final: 0.8723 (t)
REVERT: F  185 CYS cc_start: 0.8556 (m) cc_final: 0.8273 (m)
REVERT: G   68 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6600 (m-80)
REVERT: G  104 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7456 (mp10)
REVERT: H   32 GLN cc_start: 0.8554 (tp40) cc_final: 0.7661 (tm-30)
REVERT: H   68 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6390 (m-80)
REVERT: H   71 ASN cc_start: 0.8083 (m-40) cc_final: 0.7247 (t0)
REVERT: H  102 MET cc_start: 0.8467 (tpp) cc_final: 0.8250 (tpp)
REVERT: H  170 SER cc_start: 0.8943 (t) cc_final: 0.8720 (t)
REVERT: H  185 CYS cc_start: 0.8436 (m) cc_final: 0.8112 (m)
  outliers start: 50
  outliers final: 28
  residues processed: 517
  average time/residue: 0.2186
  time to fit residues: 163.3719
Evaluate side-chains
  519 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 480
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  104 GLN
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  104 GLN
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   68 TYR
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 127 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.117646 restraints weight = 23385.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120838 restraints weight = 13715.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122978 restraints weight = 10070.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12144  Z= 0.151
  Angle     :  0.878  15.113  16528  Z= 0.405
  Chirality :  0.045   0.193   1936
  Planarity :  0.005   0.058   2024
  Dihedral  :  3.966  29.087   1792
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 28.48 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.22), residues: 1480
  helix:  2.30 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -2.10 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  62 
 HIS   0.001   0.000   HIS E 166 
 PHE   0.035   0.001   PHE D  99 
 TYR   0.017   0.001   TYR D 177 
 ARG   0.002   0.000   ARG E  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    8)
  link_NAG-ASN         : angle       2.22315 (   24)
  hydrogen bonds       : bond        0.03436 (  809)
  hydrogen bonds       : angle       3.73992 ( 2427)
  SS BOND              : bond        0.00225 (   16)
  SS BOND              : angle       1.65824 (   32)
  covalent geometry    : bond        0.00365 (12120)
  covalent geometry    : angle       0.87237 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  551 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 494
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6635 (m-80)
REVERT: A   95 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8164 (tp)
REVERT: A  104 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7452 (mp10)
REVERT: B   32 GLN cc_start: 0.8558 (tp40) cc_final: 0.7661 (tm-30)
REVERT: B   68 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6351 (m-80)
REVERT: B  104 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7094 (mp-120)
REVERT: B  170 SER cc_start: 0.9041 (t) cc_final: 0.8498 (m)
REVERT: C   68 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6637 (m-80)
REVERT: C   95 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8155 (tp)
REVERT: C  104 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7382 (mp10)
REVERT: C  156 LYS cc_start: 0.8154 (mttt) cc_final: 0.7953 (mtpt)
REVERT: D   68 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6474 (m-80)
REVERT: D  102 MET cc_start: 0.8572 (tpp) cc_final: 0.8331 (tpp)
REVERT: D  104 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7104 (mp-120)
REVERT: D  170 SER cc_start: 0.8925 (t) cc_final: 0.8704 (t)
REVERT: E   68 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6647 (m-80)
REVERT: E  104 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7470 (mp10)
REVERT: E  156 LYS cc_start: 0.8160 (mttt) cc_final: 0.7949 (mtpt)
REVERT: F   68 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6404 (m-80)
REVERT: F  104 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7033 (mp-120)
REVERT: F  170 SER cc_start: 0.8979 (t) cc_final: 0.8736 (t)
REVERT: G   68 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6639 (m-80)
REVERT: G  104 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7462 (mp10)
REVERT: H   32 GLN cc_start: 0.8566 (tp40) cc_final: 0.7675 (tm-30)
REVERT: H   68 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6466 (m-80)
REVERT: H   71 ASN cc_start: 0.8150 (m-40) cc_final: 0.7246 (t0)
REVERT: H  102 MET cc_start: 0.8459 (tpp) cc_final: 0.8206 (tpp)
REVERT: H  104 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7329 (mp-120)
REVERT: H  170 SER cc_start: 0.8981 (t) cc_final: 0.8748 (t)
REVERT: H  185 CYS cc_start: 0.8560 (m) cc_final: 0.8277 (m)
  outliers start: 57
  outliers final: 37
  residues processed: 526
  average time/residue: 0.2389
  time to fit residues: 181.0680
Evaluate side-chains
  537 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 482
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  104 GLN
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  161 ASP
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   56 LEU
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  104 GLN
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain F residue  190 LEU
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  104 GLN
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  161 ASP
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   68 TYR
Chi-restraints excluded: chain H residue  104 GLN
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  161 ASP
Chi-restraints excluded: chain H residue  190 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 142 optimal weight:    0.5980
   chunk 129 optimal weight:    0.0870
   chunk 70 optimal weight:    5.9990
   chunk 149 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 19 optimal weight:   50.0000
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.153065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.121961 restraints weight = 23000.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.125105 restraints weight = 13190.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127203 restraints weight = 9521.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.6075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12144  Z= 0.157
  Angle     :  0.881  15.049  16528  Z= 0.417
  Chirality :  0.046   0.186   1936
  Planarity :  0.005   0.058   2024
  Dihedral  :  4.003  26.988   1792
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.64 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.22), residues: 1480
  helix:  2.22 (0.15), residues: 1120
  sheet:  None (None), residues: 0
  loop : -2.10 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  62 
 HIS   0.003   0.001   HIS G 166 
 PHE   0.022   0.001   PHE B  99 
 TYR   0.024   0.002   TYR D  51 
 ARG   0.005   0.000   ARG A 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    8)
  link_NAG-ASN         : angle       2.28639 (   24)
  hydrogen bonds       : bond        0.03471 (  809)
  hydrogen bonds       : angle       3.79877 ( 2427)
  SS BOND              : bond        0.00192 (   16)
  SS BOND              : angle       1.49391 (   32)
  covalent geometry    : bond        0.00381 (12120)
  covalent geometry    : angle       0.87606 (16472)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  546 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 491
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6566 (m-80)
REVERT: A  104 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7510 (mp10)
REVERT: B   68 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6356 (m-80)
REVERT: B  104 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6954 (mp-120)
REVERT: B  170 SER cc_start: 0.9008 (t) cc_final: 0.8500 (m)
REVERT: C   68 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6594 (m-80)
REVERT: C  104 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7168 (mp10)
REVERT: D   40 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7794 (t)
REVERT: D   68 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6461 (m-80)
REVERT: D  102 MET cc_start: 0.8588 (tpp) cc_final: 0.8370 (tpp)
REVERT: D  104 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7264 (mp-120)
REVERT: D  170 SER cc_start: 0.8906 (t) cc_final: 0.8681 (t)
REVERT: E   68 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6710 (m-80)
REVERT: E  104 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7497 (mp10)
REVERT: F   68 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6306 (m-80)
REVERT: F  104 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6910 (mp-120)
REVERT: F  170 SER cc_start: 0.8951 (t) cc_final: 0.8406 (m)
REVERT: G   68 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6684 (m-80)
REVERT: G  104 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7493 (mp10)
REVERT: H   32 GLN cc_start: 0.8461 (tp40) cc_final: 0.7617 (tm-30)
REVERT: H   68 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6516 (m-80)
REVERT: H   71 ASN cc_start: 0.8141 (m-40) cc_final: 0.7221 (t0)
REVERT: H  102 MET cc_start: 0.8439 (tpp) cc_final: 0.8178 (tpp)
REVERT: H  104 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7297 (mp-120)
  outliers start: 55
  outliers final: 37
  residues processed: 522
  average time/residue: 0.2192
  time to fit residues: 165.0662
Evaluate side-chains
  539 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 485
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  104 GLN
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  104 GLN
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 TYR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   68 TYR
Chi-restraints excluded: chain E residue  104 GLN
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  161 ASP
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue  104 GLN
Chi-restraints excluded: chain F residue  125 LEU
Chi-restraints excluded: chain F residue  161 ASP
Chi-restraints excluded: chain F residue  190 LEU
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain G residue   58 VAL
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain G residue   68 TYR
Chi-restraints excluded: chain G residue  104 GLN
Chi-restraints excluded: chain G residue  146 SER
Chi-restraints excluded: chain G residue  161 ASP
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   68 TYR
Chi-restraints excluded: chain H residue  104 GLN
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  161 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 151 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 108 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** B  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.154240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.123600 restraints weight = 23164.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.126770 restraints weight = 13241.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.128878 restraints weight = 9556.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.6154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12144  Z= 0.146
  Angle     :  0.889  14.975  16528  Z= 0.414
  Chirality :  0.045   0.168   1936
  Planarity :  0.005   0.058   2024
  Dihedral  :  3.991  24.307   1792
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 29.14 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.22), residues: 1480
  helix:  2.25 (0.15), residues: 1120
  sheet:  None (None), residues: 0
  loop : -2.19 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D  62 
 HIS   0.002   0.001   HIS E 166 
 PHE   0.032   0.001   PHE H  99 
 TYR   0.020   0.001   TYR D 177 
 ARG   0.004   0.000   ARG A 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    8)
  link_NAG-ASN         : angle       2.80788 (   24)
  hydrogen bonds       : bond        0.03369 (  809)
  hydrogen bonds       : angle       3.74237 ( 2427)
  SS BOND              : bond        0.00147 (   16)
  SS BOND              : angle       1.16925 (   32)
  covalent geometry    : bond        0.00342 (12120)
  covalent geometry    : angle       0.88261 (16472)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5333.65 seconds
wall clock time: 99 minutes 39.87 seconds (5979.87 seconds total)