Starting phenix.real_space_refine
on Wed Mar 12 01:09:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2025/7paf_13268.cif"
  }
  resolution = 3.75
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 892 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      24      5.16       5
     C    3992      2.51       5
     N     926      2.21       5
     O    1062      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6005
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2116
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2116
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 16
  Time building chain proxies: 5.02, per 1000 atoms: 0.84
  Number of scatterers: 6005
  At special positions: 0
  Unit cell: (102.726, 78.142, 93.946, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       1     15.00
     O    1062      8.00
     N     926      7.00
     C    3992      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  26 " - pdb=" SG  CYS B 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C 100 " 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
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      63.5% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'B' and resid 91 through 95
      removed outlier: 3.680A  pdb=" N   THR B  95 " --> pdb=" O   PRO B  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 31
      removed outlier: 4.048A  pdb=" N   LEU A  11 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR A  26 " --> pdb=" O   THR A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 59
      removed outlier: 4.149A  pdb=" N   PHE A  49 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 83 through 98
    Processing helix  chain 'A' and resid 100 through 109
    Processing helix  chain 'A' and resid 109 through 120
      removed outlier: 4.056A  pdb=" N   SER A 113 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   PHE A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 144
      removed outlier: 4.429A  pdb=" N   PHE A 131 " --> pdb=" O   LYS A 127 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLY A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 178
      removed outlier: 3.516A  pdb=" N   ALA A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   SER A 171 " --> pdb=" O   TRP A 167 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 207
      removed outlier: 3.531A  pdb=" N   LEU A 188 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG A 191 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 214
    Processing helix  chain 'A' and resid 215 through 253
      Proline residue:  A 245  - end of helix
      removed outlier: 3.582A  pdb=" N   ALA A 248 " --> pdb=" O   GLN A 244 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A 249 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLY A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASN A 252 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 266
      removed outlier: 3.603A  pdb=" N   TRP A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 289
      removed outlier: 3.524A  pdb=" N   ILE A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 95
      removed outlier: 3.674A  pdb=" N   THR C  95 " --> pdb=" O   PRO C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 31
      removed outlier: 4.077A  pdb=" N   LEU D  11 " --> pdb=" O   VAL D   7 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR D  26 " --> pdb=" O   THR D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 59
      removed outlier: 4.148A  pdb=" N   PHE D  49 " --> pdb=" O   PHE D  45 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE D  50 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 83
    Processing helix  chain 'D' and resid 83 through 98
    Processing helix  chain 'D' and resid 100 through 109
    Processing helix  chain 'D' and resid 109 through 120
      removed outlier: 4.050A  pdb=" N   SER D 113 " --> pdb=" O   TYR D 109 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   PHE D 118 " --> pdb=" O   VAL D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 144
      removed outlier: 4.424A  pdb=" N   PHE D 131 " --> pdb=" O   LYS D 127 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLY D 132 " --> pdb=" O   ASN D 128 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR D 144 " --> pdb=" O   ILE D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 178
      removed outlier: 3.516A  pdb=" N   ALA D 166 " --> pdb=" O   VAL D 162 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   SER D 171 " --> pdb=" O   TRP D 167 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   MET D 178 " --> pdb=" O   SER D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 207
      removed outlier: 3.543A  pdb=" N   LEU D 188 " --> pdb=" O   GLU D 184 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 214
      removed outlier: 3.518A  pdb=" N   VAL D 213 " --> pdb=" O   PHE D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 244
    Processing helix  chain 'D' and resid 247 through 253
      removed outlier: 3.697A  pdb=" N   ASN D 252 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 266
      removed outlier: 3.603A  pdb=" N   TRP D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 289
      removed outlier: 3.526A  pdb=" N   ILE D 276 " --> pdb=" O   ASP D 272 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 11
    Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 17
      removed outlier: 6.381A  pdb=" N   GLY B  14 " --> pdb=" O   THR B 126 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   SER B 128 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA B 101 " --> pdb=" O   GLY B  39 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR B  37 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 17
      removed outlier: 6.381A  pdb=" N   GLY B  14 " --> pdb=" O   THR B 126 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   SER B 128 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR B 118 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 11
    Processing sheet with id=AA5, first strand: chain 'C' and resid 14 through 17
      removed outlier: 6.382A  pdb=" N   GLY C  14 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   SER C 128 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA C 101 " --> pdb=" O   GLY C  39 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR C  37 " --> pdb=" O   ALA C 103 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 17
      removed outlier: 6.382A  pdb=" N   GLY C  14 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   SER C 128 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR C 118 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1170 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: 1.36

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 900
        1.32 -     1.44: 1772
        1.44 -     1.56: 3428
        1.56 -     1.68: 2
        1.68 -     1.81: 40
  Bond restraints: 6142
  Sorted by residual:
  bond pdb=" C11 PGT D 301 "
       pdb=" O3  PGT D 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.454 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C31 PGT D 301 "
       pdb=" O2  PGT D 301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.456 -0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" C   LYS D 247 "
       pdb=" O   LYS D 247 "
    ideal  model  delta    sigma   weight residual
    1.232  1.197  0.035 1.38e-02 5.25e+03 6.50e+00
  bond pdb=" C   LYS A 247 "
       pdb=" O   LYS A 247 "
    ideal  model  delta    sigma   weight residual
    1.232  1.198  0.035 1.38e-02 5.25e+03 6.35e+00
  bond pdb=" CA  PRO A 245 "
       pdb=" CB  PRO A 245 "
    ideal  model  delta    sigma   weight residual
    1.533  1.505  0.028 1.42e-02 4.96e+03 3.98e+00
  ... (remaining 6137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 8184
        1.94 -     3.89: 138
        3.89 -     5.83: 17
        5.83 -     7.77: 12
        7.77 -     9.72: 3
  Bond angle restraints: 8354
  Sorted by residual:
  angle pdb=" N   ALA A 246 "
        pdb=" CA  ALA A 246 "
        pdb=" C   ALA A 246 "
      ideal   model   delta    sigma   weight residual
     111.28  117.52   -6.24 1.09e+00 8.42e-01 3.28e+01
  angle pdb=" N   ALA D 246 "
        pdb=" CA  ALA D 246 "
        pdb=" C   ALA D 246 "
      ideal   model   delta    sigma   weight residual
     111.36  117.49   -6.13 1.09e+00 8.42e-01 3.16e+01
  angle pdb=" C   PRO A 245 "
        pdb=" N   ALA A 246 "
        pdb=" CA  ALA A 246 "
      ideal   model   delta    sigma   weight residual
     120.28  126.45   -6.17 1.34e+00 5.57e-01 2.12e+01
  angle pdb=" C   GLN A 244 "
        pdb=" N   PRO A 245 "
        pdb=" CA  PRO A 245 "
      ideal   model   delta    sigma   weight residual
     119.84  115.64    4.20 1.25e+00 6.40e-01 1.13e+01
  angle pdb=" N   GLN D 244 "
        pdb=" CA  GLN D 244 "
        pdb=" C   GLN D 244 "
      ideal   model   delta    sigma   weight residual
     109.81  117.23   -7.42 2.21e+00 2.05e-01 1.13e+01
  ... (remaining 8349 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3203
       17.31 -    34.61: 253
       34.61 -    51.92: 33
       51.92 -    69.23: 9
       69.23 -    86.53: 4
  Dihedral angle restraints: 3502
    sinusoidal: 1266
      harmonic: 2236
  Sorted by residual:
  dihedral pdb=" CA  ILE D 125 "
           pdb=" C   ILE D 125 "
           pdb=" N   SER D 126 "
           pdb=" CA  SER D 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ILE A 125 "
           pdb=" C   ILE A 125 "
           pdb=" N   SER A 126 "
           pdb=" CA  SER A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.22  -18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CB  GLU A 179 "
           pdb=" CG  GLU A 179 "
           pdb=" CD  GLU A 179 "
           pdb=" OE1 GLU A 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.63  -83.63     1      3.00e+01 1.11e-03 9.48e+00
  ... (remaining 3499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 856
       0.056 -    0.111: 129
       0.111 -    0.167: 11
       0.167 -    0.223: 0
       0.223 -    0.278: 4
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" CA  GLN A 244 "
            pdb=" N   GLN A 244 "
            pdb=" C   GLN A 244 "
            pdb=" CB  GLN A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  GLN D 244 "
            pdb=" N   GLN D 244 "
            pdb=" C   GLN D 244 "
            pdb=" CB  GLN D 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C5  PGT D 301 "
            pdb=" C4  PGT D 301 "
            pdb=" C6  PGT D 301 "
            pdb=" O5  PGT D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.56    0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 997 not shown)

  Planarity restraints: 1002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 244 "   -0.047 5.00e-02 4.00e+02   7.21e-02 8.31e+00
        pdb=" N   PRO A 245 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 245 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 245 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 244 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO D 245 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D 245 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 245 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP D 258 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.16e+00
        pdb=" C   TRP D 258 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   TRP D 258 "    0.007 2.00e-02 2.50e+03
        pdb=" N   THR D 259 "    0.006 2.00e-02 2.50e+03
  ... (remaining 999 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1324
        2.78 -     3.31: 6020
        3.31 -     3.84: 9833
        3.84 -     4.37: 11009
        4.37 -     4.90: 19546
  Nonbonded interactions: 47732
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 104 "
            pdb=" OH  TYR C 118 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD2 ASP B 104 "
            pdb=" OH  TYR B 118 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD1 ASN D 128 "
            pdb=" N   THR D 129 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OD1 ASN A 128 "
            pdb=" N   THR A 129 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OG  SER D  13 "
            pdb=" OD1 ASN D 252 "
     model   vdw
     2.388 3.040
  ... (remaining 47727 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'D' and resid 6 through 290)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             3.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.980
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
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   0.127   6142  Z= 0.280
  Angle     :  0.681   9.715   8354  Z= 0.373
  Chirality :  0.043   0.278   1000
  Planarity :  0.003   0.072   1002
  Dihedral  : 13.225  86.535   2072
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.82 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  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: -2.72 (0.26), residues: 760
  helix: -1.55 (0.21), residues: 450
  sheet: -0.63 (0.45), residues: 114
  loop : -2.66 (0.38), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  17 
 HIS   0.005   0.001   HIS A  43 
 PHE   0.009   0.001   PHE D 225 
 TYR   0.012   0.001   TYR A 255 
 ARG   0.002   0.000   ARG A 191 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    8 LEU cc_start: 0.6788 (mt) cc_final: 0.6427 (mm)
REVERT: D  184 GLU cc_start: 0.7670 (pm20) cc_final: 0.7376 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1610
  time to fit residues: 36.2056
Evaluate side-chains
  120 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0770
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
D 192 GLN
D 244 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.194747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.159775 restraints weight = 8848.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.160209 restraints weight = 7694.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.161365 restraints weight = 7157.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6142  Z= 0.214
  Angle     :  0.642   8.409   8354  Z= 0.331
  Chirality :  0.041   0.134   1000
  Planarity :  0.005   0.062   1002
  Dihedral  :  6.680  58.768    860
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.82 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.04 %
    Favored  : 79.75 %
  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: -1.06 (0.30), residues: 760
  helix: -0.19 (0.24), residues: 456
  sheet:  0.24 (0.48), residues: 114
  loop : -2.31 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 107 
 HIS   0.004   0.001   HIS D  43 
 PHE   0.016   0.001   PHE A 196 
 TYR   0.013   0.001   TYR D 109 
 ARG   0.003   0.001   ARG D  63 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.647 
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
  outliers start: 14
  outliers final: 11
  residues processed: 137
  average time/residue: 0.1348
  time to fit residues: 25.9114
Evaluate side-chains
  120 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue  172 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0010
   chunk 17 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
D  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.192046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.163717 restraints weight = 8510.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.163084 restraints weight = 12401.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163324 restraints weight = 12453.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6142  Z= 0.211
  Angle     :  0.614   7.137   8354  Z= 0.318
  Chirality :  0.040   0.133   1000
  Planarity :  0.004   0.045   1002
  Dihedral  :  6.584  57.193    860
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.00 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.89 %
    Favored  : 75.32 %
  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: -0.44 (0.31), residues: 760
  helix:  0.28 (0.25), residues: 458
  sheet:  0.59 (0.50), residues: 114
  loop : -2.09 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 107 
 HIS   0.005   0.001   HIS D  43 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.012   0.001   TYR D 109 
 ARG   0.002   0.000   ARG A  63 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.653 
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: D  261 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7987 (tp)
  outliers start: 24
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1358
  time to fit residues: 27.1186
Evaluate side-chains
  129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain B residue  112 TYR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  261 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0010
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.193266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.165757 restraints weight = 8876.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.164888 restraints weight = 14588.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165165 restraints weight = 14357.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6142  Z= 0.240
  Angle     :  0.649   7.312   8354  Z= 0.333
  Chirality :  0.041   0.136   1000
  Planarity :  0.004   0.044   1002
  Dihedral  :  6.714  56.812    860
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 22.47 %
    Favored  : 73.42 %
  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: -0.20 (0.31), residues: 760
  helix:  0.46 (0.25), residues: 458
  sheet:  0.65 (0.49), residues: 114
  loop : -1.95 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 107 
 HIS   0.007   0.001   HIS D  43 
 PHE   0.014   0.001   PHE D   9 
 TYR   0.014   0.002   TYR D 109 
 ARG   0.002   0.000   ARG A  63 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.661 
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  222 MET cc_start: 0.7534 (mmm) cc_final: 0.7287 (mmm)
REVERT: D  230 MET cc_start: 0.7812 (tpp) cc_final: 0.7473 (mmp)
  outliers start: 26
  outliers final: 16
  residues processed: 140
  average time/residue: 0.1513
  time to fit residues: 29.0956
Evaluate side-chains
  130 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  172 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0010
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0980
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0980
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0000
   overall best weight:    0.1590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.195944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.163406 restraints weight = 8603.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.164121 restraints weight = 7319.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.164407 restraints weight = 6462.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6142  Z= 0.171
  Angle     :  0.619   7.200   8354  Z= 0.311
  Chirality :  0.039   0.133   1000
  Planarity :  0.003   0.038   1002
  Dihedral  :  6.539  58.383    860
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 24.84 %
    Favored  : 72.31 %
  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:  0.29 (0.32), residues: 760
  helix:  0.83 (0.25), residues: 458
  sheet:  1.00 (0.50), residues: 114
  loop : -1.85 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  17 
 HIS   0.001   0.000   HIS D  43 
 PHE   0.027   0.001   PHE B  72 
 TYR   0.017   0.001   TYR A 287 
 ARG   0.002   0.000   ARG D  63 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 MET cc_start: 0.3930 (ptm) cc_final: 0.3665 (ptm)
REVERT: A   87 MET cc_start: 0.7022 (mpp) cc_final: 0.6054 (mtt)
REVERT: C  108 MET cc_start: 0.3912 (ptm) cc_final: 0.3654 (ptm)
REVERT: D   87 MET cc_start: 0.7112 (mpp) cc_final: 0.6122 (mtt)
REVERT: D  230 MET cc_start: 0.7719 (tpp) cc_final: 0.7435 (mmp)
  outliers start: 18
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1549
  time to fit residues: 27.5493
Evaluate side-chains
  129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  136 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 59 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0970
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 ASN
** C 124 GLN ** 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 = 0.4516 r_free = 0.4516 target = 0.195907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.160825 restraints weight = 8881.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.161605 restraints weight = 7784.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.162077 restraints weight = 7115.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6142  Z= 0.228
  Angle     :  0.662   8.282   8354  Z= 0.335
  Chirality :  0.041   0.134   1000
  Planarity :  0.003   0.037   1002
  Dihedral  :  6.690  58.296    860
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.32 %
    Favored  : 71.04 %
  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:  0.32 (0.32), residues: 760
  helix:  0.85 (0.25), residues: 458
  sheet:  1.12 (0.52), residues: 114
  loop : -1.88 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  17 
 HIS   0.005   0.001   HIS D  43 
 PHE   0.040   0.002   PHE C  72 
 TYR   0.013   0.002   TYR D 109 
 ARG   0.002   0.000   ARG D 191 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 MET cc_start: 0.7008 (mpp) cc_final: 0.6224 (mtt)
REVERT: D   43 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7780 (t-170)
REVERT: D   87 MET cc_start: 0.7036 (mpp) cc_final: 0.6247 (mtt)
REVERT: D  230 MET cc_start: 0.7802 (tpp) cc_final: 0.7557 (mmp)
  outliers start: 23
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1494
  time to fit residues: 28.2260
Evaluate side-chains
  128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 VAL
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   81 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 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 = 0.4484 r_free = 0.4484 target = 0.189307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.160158 restraints weight = 8568.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.159072 restraints weight = 11722.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.159708 restraints weight = 10397.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6142  Z= 0.282
  Angle     :  0.703   8.354   8354  Z= 0.359
  Chirality :  0.042   0.171   1000
  Planarity :  0.003   0.035   1002
  Dihedral  :  7.006  59.484    860
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.16 %
    Favored  : 71.20 %
  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:  0.14 (0.31), residues: 760
  helix:  0.71 (0.25), residues: 458
  sheet:  0.88 (0.57), residues: 98
  loop : -1.60 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  17 
 HIS   0.007   0.001   HIS D  43 
 PHE   0.026   0.002   PHE C  72 
 TYR   0.015   0.002   TYR A 109 
 ARG   0.004   0.001   ARG C  23 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 MET cc_start: 0.4037 (ptm) cc_final: 0.3717 (ptm)
REVERT: A   43 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7751 (t-170)
REVERT: A  230 MET cc_start: 0.7887 (tpp) cc_final: 0.7604 (mmp)
REVERT: D   43 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7774 (t-170)
REVERT: D  230 MET cc_start: 0.7947 (tpp) cc_final: 0.7730 (mmp)
  outliers start: 23
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1550
  time to fit residues: 29.1358
Evaluate side-chains
  131 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   43 HIS
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  172 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0370
   chunk 73 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0770
   chunk 56 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 15 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.2816

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

Flipped N/Q/H residues before XYZ refinement:
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 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 = 0.4545 r_free = 0.4545 target = 0.195520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.166323 restraints weight = 8484.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.161431 restraints weight = 9009.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.162234 restraints weight = 7531.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6142  Z= 0.191
  Angle     :  0.672   9.857   8354  Z= 0.336
  Chirality :  0.041   0.167   1000
  Planarity :  0.003   0.035   1002
  Dihedral  :  6.846  56.920    860
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 28.01 %
    Favored  : 69.62 %
  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 (0.32), residues: 760
  helix:  0.92 (0.25), residues: 460
  sheet:  0.94 (0.57), residues: 98
  loop : -1.66 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  17 
 HIS   0.002   0.001   HIS D  43 
 PHE   0.009   0.001   PHE B  72 
 TYR   0.019   0.001   TYR C  63 
 ARG   0.001   0.000   ARG D 191 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 MET cc_start: 0.7762 (tpp) cc_final: 0.7507 (mmp)
REVERT: C   23 ARG cc_start: 0.6925 (mmm160) cc_final: 0.6221 (tpp80)
REVERT: D  230 MET cc_start: 0.7789 (tpp) cc_final: 0.7580 (mmp)
  outliers start: 15
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1528
  time to fit residues: 27.4235
Evaluate side-chains
  130 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   81 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0170
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.9824

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.189096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.160835 restraints weight = 8528.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.159461 restraints weight = 12994.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.160035 restraints weight = 10906.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6142  Z= 0.318
  Angle     :  0.732   8.604   8354  Z= 0.372
  Chirality :  0.043   0.168   1000
  Planarity :  0.003   0.035   1002
  Dihedral  :  7.187  59.764    860
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.42 %
    Favored  : 69.62 %
  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:  0.03 (0.31), residues: 760
  helix:  0.60 (0.25), residues: 460
  sheet:  0.85 (0.56), residues: 98
  loop : -1.62 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C 107 
 HIS   0.008   0.001   HIS D  43 
 PHE   0.019   0.002   PHE D 225 
 TYR   0.020   0.002   TYR D 287 
 ARG   0.003   0.001   ARG D 191 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (t-170)
REVERT: A  230 MET cc_start: 0.7868 (tpp) cc_final: 0.7591 (mmp)
REVERT: C   23 ARG cc_start: 0.6276 (mmm160) cc_final: 0.5556 (tpp80)
REVERT: D  230 MET cc_start: 0.7952 (tpp) cc_final: 0.7724 (mmp)
  outliers start: 25
  outliers final: 21
  residues processed: 132
  average time/residue: 0.1502
  time to fit residues: 27.2620
Evaluate side-chains
  139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 32 optimal weight:    0.3980
   chunk 39 optimal weight:   10.0000
   chunk 43 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.192413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.164517 restraints weight = 8619.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.163324 restraints weight = 12647.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.163849 restraints weight = 10073.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6142  Z= 0.225
  Angle     :  0.735  12.134   8354  Z= 0.366
  Chirality :  0.043   0.179   1000
  Planarity :  0.003   0.035   1002
  Dihedral  :  7.107  59.622    860
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 28.80 %
    Favored  : 68.35 %
  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:  0.15 (0.32), residues: 760
  helix:  0.72 (0.25), residues: 460
  sheet:  0.91 (0.56), residues: 98
  loop : -1.67 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP C 107 
 HIS   0.004   0.001   HIS D  43 
 PHE   0.011   0.001   PHE D  54 
 TYR   0.021   0.002   TYR D 287 
 ARG   0.002   0.000   ARG A 191 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7701 (t-170)
REVERT: A  230 MET cc_start: 0.7782 (tpp) cc_final: 0.7545 (mmp)
REVERT: C   23 ARG cc_start: 0.6297 (mmm160) cc_final: 0.5755 (tpp80)
REVERT: D  230 MET cc_start: 0.7815 (tpp) cc_final: 0.7589 (mmp)
  outliers start: 18
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1567
  time to fit residues: 27.7866
Evaluate side-chains
  134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue   99 TYR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue    7 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   81 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.0870
   chunk 66 optimal weight:    0.0770
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.5716

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.191840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.162777 restraints weight = 8737.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.161485 restraints weight = 12287.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.162249 restraints weight = 10810.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6142  Z= 0.243
  Angle     :  0.730  11.428   8354  Z= 0.368
  Chirality :  0.042   0.177   1000
  Planarity :  0.003   0.036   1002
  Dihedral  :  7.030  56.996    860
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 28.01 %
    Favored  : 68.83 %
  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:  0.05 (0.31), residues: 760
  helix:  0.66 (0.25), residues: 460
  sheet:  0.79 (0.55), residues: 98
  loop : -1.70 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C 107 
 HIS   0.005   0.001   HIS D  43 
 PHE   0.011   0.001   PHE D 225 
 TYR   0.020   0.002   TYR D 287 
 ARG   0.002   0.000   ARG A 191 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2123.61 seconds
wall clock time: 37 minutes 44.60 seconds (2264.60 seconds total)