Starting phenix.real_space_refine
on Tue Mar  3 12:08:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sod_25267/03_2026/7sod_25267.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.089
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      15      5.16       5
     C    2464      2.51       5
     N     617      2.21       5
     O     734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3830
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 940
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1960
          Classifications: {'peptide': 245}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 14, 'TRANS': 230}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 0.96, per 1000 atoms: 0.25
  Number of scatterers: 3830
  At special positions: 0
  Unit cell: (83.457, 70.812, 76.713, 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      15     16.00
     O     734      8.00
     N     617      7.00
     C    2464      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.02

  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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 234 "
      " NAG A1303 " - " ASN A 282 "
      " NAG A1304 " - " ASN A  17 "
      " NAG A1305 " - " ASN A 165 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 141.7 milliseconds
  

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  882

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 10 sheets defined
      4.2% alpha, 58.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'A' and resid 294 through 303
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.802A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LEU L  33 " --> pdb=" O   SER L  49 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   SER L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.802A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.662A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31
      removed outlier: 3.962A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER A  60 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55
      removed outlier: 7.323A  pdb=" N   THR A 274 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ASP A 290 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU A 276 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.296A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   TYR A 170 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   PHE A 168 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER A 162 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TYR A 160 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASP A 138 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ARG A 158 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   PHE A 140 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   GLU A 156 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 13.023A  pdb=" N   PHE A 238 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 12.887A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 12.848A  pdb=" N   THR A 240 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 11.280A  pdb=" N   ASN A 137 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 11.472A  pdb=" N   LEU A 242 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   TYR A 170 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   PHE A 168 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER A 162 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TYR A 160 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASP A 138 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ARG A 158 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   PHE A 140 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   GLU A 156 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)

    162 hydrogen bonds defined for protein.
    387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.56

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 654
        1.32 -     1.45: 1111
        1.45 -     1.57: 2139
        1.57 -     1.70: 2
        1.70 -     1.82: 20
  Bond restraints: 3926
  Sorted by residual:
  bond pdb=" CA  SER A  31 "
       pdb=" CB  SER A  31 "
    ideal  model  delta    sigma   weight residual
    1.530  1.460  0.070 1.69e-02 3.50e+03 1.73e+01
  bond pdb=" C   PHE A  32 "
       pdb=" O   PHE A  32 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.15e-02 7.56e+03 1.44e+01
  bond pdb=" C   TRP L   3 "
       pdb=" O   TRP L   3 "
    ideal  model  delta    sigma   weight residual
    1.234  1.199  0.036 1.22e-02 6.72e+03 8.64e+00
  bond pdb=" C5  NAG A1304 "
       pdb=" O5  NAG A1304 "
    ideal  model  delta    sigma   weight residual
    1.413  1.468 -0.055 2.00e-02 2.50e+03 7.53e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.42e+00
  ... (remaining 3921 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 4900
        2.04 -     4.09: 354
        4.09 -     6.13: 57
        6.13 -     8.18: 20
        8.18 -    10.22: 1
  Bond angle restraints: 5332
  Sorted by residual:
  angle pdb=" C   LEU A  24 "
        pdb=" N   PRO A  25 "
        pdb=" CA  PRO A  25 "
      ideal   model   delta    sigma   weight residual
     119.66  126.08   -6.42 7.20e-01 1.93e+00 7.95e+01
  angle pdb=" C   ASP A 138 "
        pdb=" N   PRO A 139 "
        pdb=" CA  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     119.76  127.18   -7.42 1.00e+00 1.00e+00 5.50e+01
  angle pdb=" C   PRO A  25 "
        pdb=" N   PRO A  26 "
        pdb=" CA  PRO A  26 "
      ideal   model   delta    sigma   weight residual
     119.85  126.79   -6.94 1.01e+00 9.80e-01 4.73e+01
  angle pdb=" C   GLY L  99 "
        pdb=" N   PRO L 100 "
        pdb=" CA  PRO L 100 "
      ideal   model   delta    sigma   weight residual
     119.32  127.13   -7.81 1.14e+00 7.69e-01 4.69e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  126.77   -6.74 9.90e-01 1.02e+00 4.63e+01
  ... (remaining 5327 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.77: 2235
       12.77 -    25.53: 112
       25.53 -    38.29: 25
       38.29 -    51.06: 10
       51.06 -    63.82: 8
  Dihedral angle restraints: 2390
    sinusoidal: 1014
      harmonic: 1376
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.17   41.83     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CA  TYR H  95 "
           pdb=" C   TYR H  95 "
           pdb=" N   CYS H  96 "
           pdb=" CA  CYS H  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  THR A 208 "
           pdb=" C   THR A 208 "
           pdb=" N   PRO A 209 "
           pdb=" CA  PRO A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.17   15.83     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 2387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 422
       0.066 -    0.132: 139
       0.132 -    0.198: 27
       0.198 -    0.264: 9
       0.264 -    0.330: 8
  Chirality restraints: 605
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.47    0.07 2.00e-02 2.50e+03 1.34e+01
  chirality pdb=" C2  NAG B   2 "
            pdb=" C1  NAG B   2 "
            pdb=" C3  NAG B   2 "
            pdb=" N2  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.82    0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" C2  NAG A1305 "
            pdb=" C1  NAG A1305 "
            pdb=" C3  NAG A1305 "
            pdb=" N2  NAG A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.81    0.32 2.00e-01 2.50e+01 2.57e+00
  ... (remaining 602 not shown)

  Planarity restraints: 675
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  31 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.89e+00
        pdb=" C   SER A  31 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   SER A  31 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A  32 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 305 "   -0.011 2.00e-02 2.50e+03   2.32e-02 5.38e+00
        pdb=" C   SER A 305 "    0.040 2.00e-02 2.50e+03
        pdb=" O   SER A 305 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 306 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  32 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   PHE A  32 "    0.036 2.00e-02 2.50e+03
        pdb=" O   PHE A  32 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR A  33 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 672 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 58
        2.68 -     3.24: 3365
        3.24 -     3.79: 5626
        3.79 -     4.35: 8285
        4.35 -     4.90: 13643
  Nonbonded interactions: 30977
  Sorted by model distance:
  nonbonded pdb=" O   SER A  31 "
            pdb=" OG  SER A  31 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" O   ASP L  92 "
            pdb=" NH1 ARG H 103 "
     model   vdw
     2.524 3.120
  nonbonded pdb=" ND2 ASN A  81 "
            pdb=" O   THR A 240 "
     model   vdw
     2.554 3.120
  nonbonded pdb=" N   TYR A 144 "
            pdb=" O   TYR A 144 "
     model   vdw
     2.584 2.496
  nonbonded pdb=" C   SER A  31 "
            pdb=" OG  SER A  31 "
     model   vdw
     2.601 2.616
  ... (remaining 30972 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.880
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.440
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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      :  0.011   0.070   3938  Z= 0.608
  Angle     :  1.253  10.221   5363  Z= 0.831
  Chirality :  0.076   0.330    605
  Planarity :  0.005   0.026    669
  Dihedral  :  9.166  63.823   1493
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 0.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  0.25 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.38), residues: 457
  helix:  0.51 (1.78), residues: 11
  sheet:  1.07 (0.34), residues: 214
  loop :  0.41 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  61 
 TYR   0.024   0.004   TYR A 269 
 PHE   0.015   0.003   PHE A  55 
 TRP   0.022   0.004   TRP H  47 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.01108 ( 3926)
  covalent geometry    : angle       1.24357 ( 5332)
  SS BOND              : bond        0.00654 (    5)
  SS BOND              : angle       2.78480 (   10)
  hydrogen bonds       : bond        0.16005 (  148)
  hydrogen bonds       : angle       9.02307 (  387)
  link_BETA1-4         : bond        0.05222 (    1)
  link_BETA1-4         : angle       2.70978 (    3)
  link_NAG-ASN         : bond        0.05655 (    6)
  link_NAG-ASN         : angle       2.11432 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  177 MET cc_start: 0.5837 (mpp) cc_final: 0.5040 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1138
  time to fit residues: 8.3533
Evaluate side-chains
  44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.112550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.091821 restraints weight = 4333.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.46
r_work: 0.2737 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3938  Z= 0.140
  Angle     :  0.563   7.394   5363  Z= 0.293
  Chirality :  0.045   0.151    605
  Planarity :  0.004   0.030    669
  Dihedral  :  4.789  32.979    658
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.17 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.40), residues: 457
  helix:  2.13 (1.79), residues: 11
  sheet:  1.24 (0.34), residues: 228
  loop :  0.63 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 102 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.013   0.002   PHE A 220 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3926)
  covalent geometry    : angle       0.55219 ( 5332)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       0.79373 (   10)
  hydrogen bonds       : bond        0.03701 (  148)
  hydrogen bonds       : angle       6.46797 (  387)
  link_BETA1-4         : bond        0.00799 (    1)
  link_BETA1-4         : angle       1.50927 (    3)
  link_NAG-ASN         : bond        0.00566 (    6)
  link_NAG-ASN         : angle       1.85830 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.8978 (mmm) cc_final: 0.8242 (mmm)
REVERT: A  100 ILE cc_start: 0.8381 (mm) cc_final: 0.8133 (mp)
REVERT: A  108 THR cc_start: 0.8856 (p) cc_final: 0.8605 (p)
REVERT: A  177 MET cc_start: 0.6676 (mpp) cc_final: 0.5481 (mmt)
REVERT: A  207 HIS cc_start: 0.8465 (t-170) cc_final: 0.7330 (m170)
  outliers start: 3
  outliers final: 2
  residues processed: 45
  average time/residue: 0.1050
  time to fit residues: 5.6963
Evaluate side-chains
  42 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain A residue  287 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
H  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.104832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.081929 restraints weight = 4394.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 1.63
r_work: 0.2614 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   3938  Z= 0.277
  Angle     :  0.630   6.118   5363  Z= 0.328
  Chirality :  0.049   0.166    605
  Planarity :  0.005   0.030    669
  Dihedral  :  5.074  40.587    658
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.41 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.39), residues: 457
  helix:  2.68 (1.65), residues: 11
  sheet:  1.06 (0.34), residues: 220
  loop :  0.39 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 102 
 TYR   0.020   0.002   TYR A 265 
 PHE   0.019   0.003   PHE L  98 
 TRP   0.022   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 ( 3926)
  covalent geometry    : angle       0.62306 ( 5332)
  SS BOND              : bond        0.00439 (    5)
  SS BOND              : angle       1.05494 (   10)
  hydrogen bonds       : bond        0.04112 (  148)
  hydrogen bonds       : angle       6.11866 (  387)
  link_BETA1-4         : bond        0.00312 (    1)
  link_BETA1-4         : angle       0.75023 (    3)
  link_NAG-ASN         : bond        0.00318 (    6)
  link_NAG-ASN         : angle       1.60570 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.129 
Fit side-chains
REVERT: L   54 MET cc_start: 0.8326 (mmm) cc_final: 0.7961 (mmm)
REVERT: A  177 MET cc_start: 0.6761 (mpp) cc_final: 0.5784 (mmm)
REVERT: A  187 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7760 (mtmm)
REVERT: A  207 HIS cc_start: 0.8490 (t-170) cc_final: 0.7109 (m170)
REVERT: A  273 ARG cc_start: 0.8628 (mmt180) cc_final: 0.8361 (mmt180)
  outliers start: 3
  outliers final: 3
  residues processed: 44
  average time/residue: 0.1005
  time to fit residues: 5.3599
Evaluate side-chains
  44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.106326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.085276 restraints weight = 4392.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 1.66
r_work: 0.2626 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2495 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3938  Z= 0.166
  Angle     :  0.523   5.511   5363  Z= 0.273
  Chirality :  0.045   0.158    605
  Planarity :  0.004   0.028    669
  Dihedral  :  4.675  36.780    658
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  6.86 %
    Favored  : 92.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.40), residues: 457
  helix:  2.88 (1.66), residues: 11
  sheet:  1.01 (0.34), residues: 220
  loop :  0.48 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 102 
 TYR   0.017   0.001   TYR A 265 
 PHE   0.013   0.002   PHE H  50 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3926)
  covalent geometry    : angle       0.51579 ( 5332)
  SS BOND              : bond        0.00235 (    5)
  SS BOND              : angle       0.48452 (   10)
  hydrogen bonds       : bond        0.03319 (  148)
  hydrogen bonds       : angle       5.78652 (  387)
  link_BETA1-4         : bond        0.00334 (    1)
  link_BETA1-4         : angle       0.79114 (    3)
  link_NAG-ASN         : bond        0.00378 (    6)
  link_NAG-ASN         : angle       1.53272 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.146 
Fit side-chains
REVERT: L   54 MET cc_start: 0.8259 (mmm) cc_final: 0.8021 (mmm)
REVERT: A  207 HIS cc_start: 0.8495 (t-170) cc_final: 0.7245 (m170)
REVERT: A  273 ARG cc_start: 0.8667 (mmt180) cc_final: 0.8424 (mtt180)
  outliers start: 1
  outliers final: 1
  residues processed: 39
  average time/residue: 0.1023
  time to fit residues: 4.8055
Evaluate side-chains
  37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0010
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.105541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.084150 restraints weight = 4464.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 1.52
r_work: 0.2626 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2497 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3938  Z= 0.166
  Angle     :  0.517   5.933   5363  Z= 0.269
  Chirality :  0.045   0.159    605
  Planarity :  0.004   0.026    669
  Dihedral  :  4.454  31.293    658
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.62 %
    Favored  : 92.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.40), residues: 457
  helix:  3.02 (1.69), residues: 11
  sheet:  0.92 (0.36), residues: 211
  loop :  0.52 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 102 
 TYR   0.017   0.001   TYR A 265 
 PHE   0.014   0.002   PHE H  50 
 TRP   0.015   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 3926)
  covalent geometry    : angle       0.51218 ( 5332)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       0.48223 (   10)
  hydrogen bonds       : bond        0.03224 (  148)
  hydrogen bonds       : angle       5.61731 (  387)
  link_BETA1-4         : bond        0.00264 (    1)
  link_BETA1-4         : angle       0.77355 (    3)
  link_NAG-ASN         : bond        0.00205 (    6)
  link_NAG-ASN         : angle       1.28373 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  177 MET cc_start: 0.6844 (mpp) cc_final: 0.5706 (mmm)
REVERT: A  207 HIS cc_start: 0.8426 (t-170) cc_final: 0.7125 (m170)
REVERT: A  273 ARG cc_start: 0.8647 (mmt180) cc_final: 0.8439 (mtt180)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1047
  time to fit residues: 4.8888
Evaluate side-chains
  39 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.106336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.083721 restraints weight = 4538.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 1.69
r_work: 0.2620 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3938  Z= 0.163
  Angle     :  0.511   5.875   5363  Z= 0.267
  Chirality :  0.044   0.160    605
  Planarity :  0.004   0.029    669
  Dihedral  :  4.464  32.787    658
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.86 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.40), residues: 457
  helix:  2.97 (1.69), residues: 11
  sheet:  0.90 (0.36), residues: 211
  loop :  0.49 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.017   0.001   TYR A 265 
 PHE   0.013   0.002   PHE H  50 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3926)
  covalent geometry    : angle       0.50589 ( 5332)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.40641 (   10)
  hydrogen bonds       : bond        0.03176 (  148)
  hydrogen bonds       : angle       5.54977 (  387)
  link_BETA1-4         : bond        0.00101 (    1)
  link_BETA1-4         : angle       0.68100 (    3)
  link_NAG-ASN         : bond        0.00191 (    6)
  link_NAG-ASN         : angle       1.35588 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7039 (mpp) cc_final: 0.5853 (mmm)
REVERT: A  207 HIS cc_start: 0.8453 (t-170) cc_final: 0.7195 (m170)
  outliers start: 4
  outliers final: 2
  residues processed: 40
  average time/residue: 0.1063
  time to fit residues: 5.0567
Evaluate side-chains
  39 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.106911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.084569 restraints weight = 4564.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 1.73
r_work: 0.2611 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2476 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3938  Z= 0.149
  Angle     :  0.501   5.870   5363  Z= 0.262
  Chirality :  0.044   0.159    605
  Planarity :  0.004   0.026    669
  Dihedral  :  4.337  29.009    658
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.33 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.40), residues: 457
  helix:  2.99 (1.70), residues: 11
  sheet:  0.91 (0.36), residues: 211
  loop :  0.50 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.017   0.001   TYR A 265 
 PHE   0.012   0.002   PHE H  50 
 TRP   0.013   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3926)
  covalent geometry    : angle       0.49537 ( 5332)
  SS BOND              : bond        0.00214 (    5)
  SS BOND              : angle       0.35913 (   10)
  hydrogen bonds       : bond        0.03079 (  148)
  hydrogen bonds       : angle       5.48668 (  387)
  link_BETA1-4         : bond        0.00333 (    1)
  link_BETA1-4         : angle       0.82193 (    3)
  link_NAG-ASN         : bond        0.00164 (    6)
  link_NAG-ASN         : angle       1.34225 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.107 
Fit side-chains
REVERT: L   61 ARG cc_start: 0.8287 (ptt-90) cc_final: 0.8037 (ptt-90)
REVERT: A  177 MET cc_start: 0.7024 (mpp) cc_final: 0.5872 (mmm)
REVERT: A  207 HIS cc_start: 0.8472 (t-170) cc_final: 0.7205 (m170)
  outliers start: 3
  outliers final: 3
  residues processed: 40
  average time/residue: 0.1138
  time to fit residues: 5.3217
Evaluate side-chains
  40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 44 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.106432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.083842 restraints weight = 4491.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 1.65
r_work: 0.2624 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2491 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3938  Z= 0.170
  Angle     :  0.519   6.038   5363  Z= 0.270
  Chirality :  0.045   0.163    605
  Planarity :  0.004   0.028    669
  Dihedral  :  4.365  24.474    658
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.33 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.40), residues: 457
  helix:  3.01 (1.70), residues: 11
  sheet:  0.84 (0.36), residues: 211
  loop :  0.42 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.018   0.001   TYR A 265 
 PHE   0.013   0.002   PHE A 133 
 TRP   0.015   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3926)
  covalent geometry    : angle       0.51276 ( 5332)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.45328 (   10)
  hydrogen bonds       : bond        0.03227 (  148)
  hydrogen bonds       : angle       5.48999 (  387)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       0.80236 (    3)
  link_NAG-ASN         : bond        0.00090 (    6)
  link_NAG-ASN         : angle       1.41641 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.107 
Fit side-chains
REVERT: L   61 ARG cc_start: 0.8254 (ptt-90) cc_final: 0.7833 (ptt-90)
REVERT: A  177 MET cc_start: 0.7019 (mpp) cc_final: 0.5842 (mmm)
REVERT: A  207 HIS cc_start: 0.8427 (t-170) cc_final: 0.7170 (m170)
  outliers start: 3
  outliers final: 3
  residues processed: 36
  average time/residue: 0.1053
  time to fit residues: 4.5058
Evaluate side-chains
  37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.110376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.084498 restraints weight = 4372.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 1.96
r_work: 0.2611 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2466 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3938  Z= 0.213
  Angle     :  0.546   6.212   5363  Z= 0.284
  Chirality :  0.046   0.166    605
  Planarity :  0.004   0.026    669
  Dihedral  :  4.499  29.221    658
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.33 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.40), residues: 457
  helix:  3.02 (1.70), residues: 11
  sheet:  0.76 (0.35), residues: 211
  loop :  0.33 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 102 
 TYR   0.019   0.002   TYR A 265 
 PHE   0.014   0.002   PHE A 133 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 3926)
  covalent geometry    : angle       0.54085 ( 5332)
  SS BOND              : bond        0.00309 (    5)
  SS BOND              : angle       0.46935 (   10)
  hydrogen bonds       : bond        0.03422 (  148)
  hydrogen bonds       : angle       5.55651 (  387)
  link_BETA1-4         : bond        0.00163 (    1)
  link_BETA1-4         : angle       0.86904 (    3)
  link_NAG-ASN         : bond        0.00113 (    6)
  link_NAG-ASN         : angle       1.42346 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  177 MET cc_start: 0.6949 (mpp) cc_final: 0.5788 (mmm)
REVERT: A  207 HIS cc_start: 0.8458 (t-170) cc_final: 0.7095 (m170)
  outliers start: 3
  outliers final: 3
  residues processed: 34
  average time/residue: 0.1042
  time to fit residues: 4.2856
Evaluate side-chains
  34 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0030
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.2790

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
H  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.108298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.085083 restraints weight = 4495.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 1.64
r_work: 0.2649 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2514 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3938  Z= 0.103
  Angle     :  0.465   5.136   5363  Z= 0.244
  Chirality :  0.043   0.150    605
  Planarity :  0.004   0.028    669
  Dihedral  :  4.142  25.879    658
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  8.82 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.40), residues: 457
  helix:  2.89 (1.68), residues: 11
  sheet:  0.84 (0.36), residues: 206
  loop :  0.33 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.015   0.001   TYR A 265 
 PHE   0.010   0.001   PHE H  50 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3926)
  covalent geometry    : angle       0.45987 ( 5332)
  SS BOND              : bond        0.00151 (    5)
  SS BOND              : angle       0.26791 (   10)
  hydrogen bonds       : bond        0.02766 (  148)
  hydrogen bonds       : angle       5.34466 (  387)
  link_BETA1-4         : bond        0.00375 (    1)
  link_BETA1-4         : angle       0.87415 (    3)
  link_NAG-ASN         : bond        0.00148 (    6)
  link_NAG-ASN         : angle       1.31656 (   18)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.151 
Fit side-chains
REVERT: L   61 ARG cc_start: 0.8183 (ptt-90) cc_final: 0.7781 (ptt-90)
REVERT: A  177 MET cc_start: 0.6993 (mpp) cc_final: 0.5859 (mmt)
REVERT: A  205 SER cc_start: 0.9201 (p) cc_final: 0.8961 (t)
REVERT: A  207 HIS cc_start: 0.8430 (t-170) cc_final: 0.7159 (m170)
  outliers start: 2
  outliers final: 2
  residues processed: 40
  average time/residue: 0.0967
  time to fit residues: 4.7078
Evaluate side-chains
  41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  167 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0980
   chunk 22 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 40 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
H  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.108840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.086131 restraints weight = 4409.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 1.68
r_work: 0.2672 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3938  Z= 0.109
  Angle     :  0.465   5.600   5363  Z= 0.244
  Chirality :  0.043   0.152    605
  Planarity :  0.004   0.025    669
  Dihedral  :  3.972  24.315    658
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  8.82 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.40), residues: 457
  helix:  2.80 (1.66), residues: 11
  sheet:  0.83 (0.36), residues: 206
  loop :  0.40 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.016   0.001   TYR A 265 
 PHE   0.010   0.001   PHE H  50 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3926)
  covalent geometry    : angle       0.46002 ( 5332)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.30849 (   10)
  hydrogen bonds       : bond        0.02780 (  148)
  hydrogen bonds       : angle       5.25851 (  387)
  link_BETA1-4         : bond        0.00318 (    1)
  link_BETA1-4         : angle       0.87717 (    3)
  link_NAG-ASN         : bond        0.00151 (    6)
  link_NAG-ASN         : angle       1.30071 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1294.16 seconds
wall clock time: 22 minutes 46.72 seconds (1366.72 seconds total)