Starting phenix.real_space_refine
on Fri Aug 22 18:16:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcl_29934/08_2025/8gcl_29934.map"
  }
  resolution = 2.89
  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=   0.053 sd=   0.213
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      24      5.16       5
     C    4588      2.51       5
     N    1172      2.21       5
     O    1232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1754
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 227}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.39, per 1000 atoms: 0.20
  Number of scatterers: 7016
  At special positions: 0
  Unit cell: (85.44, 85.44, 66.24, 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      24     16.00
     O    1232      8.00
     N    1172      7.00
     C    4588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.44
  Conformation dependent library (CDL) restraints added in 264.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      79.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.550A  pdb=" N   GLY A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A  30 " --> pdb=" O   PHE A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 64
      removed outlier: 3.592A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   HIS A  61 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ILE A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 78
    Processing helix  chain 'A' and resid 82 through 108
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 4.287A  pdb=" N   GLY A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 149
      removed outlier: 3.684A  pdb=" N   THR A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.581A  pdb=" N   GLY A 154 " --> pdb=" O   GLU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.759A  pdb=" N   LEU A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   HIS A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
      Proline residue:  A 191  - end of helix
      removed outlier: 3.796A  pdb=" N   VAL A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 222
      Proline residue:  A 208  - end of helix
    Processing helix  chain 'A' and resid 229 through 238
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.550A  pdb=" N   GLY B  29 " --> pdb=" O   PHE B  25 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER B  30 " --> pdb=" O   PHE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 64
      removed outlier: 3.592A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   HIS B  61 " --> pdb=" O   GLN B  57 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ILE B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 78
    Processing helix  chain 'B' and resid 82 through 108
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 4.287A  pdb=" N   GLY B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 149
      removed outlier: 3.684A  pdb=" N   THR B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 154
      removed outlier: 3.581A  pdb=" N   GLY B 154 " --> pdb=" O   GLU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 180
      removed outlier: 3.759A  pdb=" N   LEU B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   HIS B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 196
      Proline residue:  B 191  - end of helix
      removed outlier: 3.796A  pdb=" N   VAL B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 222
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 229 through 238
    Processing helix  chain 'C' and resid 6 through 31
      removed outlier: 3.550A  pdb=" N   GLY C  29 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER C  30 " --> pdb=" O   PHE C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 64
      removed outlier: 3.592A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   HIS C  61 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ILE C  62 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 78
    Processing helix  chain 'C' and resid 82 through 108
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 4.287A  pdb=" N   GLY C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 149
      removed outlier: 3.684A  pdb=" N   THR C 132 " --> pdb=" O   GLY C 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 154
      removed outlier: 3.581A  pdb=" N   GLY C 154 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.759A  pdb=" N   LEU C 174 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   HIS C 177 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR C 178 " --> pdb=" O   LEU C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 196
      Proline residue:  C 191  - end of helix
      removed outlier: 3.796A  pdb=" N   VAL C 194 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 222
      Proline residue:  C 208  - end of helix
    Processing helix  chain 'C' and resid 229 through 238
    Processing helix  chain 'D' and resid 6 through 31
      removed outlier: 3.550A  pdb=" N   GLY D  29 " --> pdb=" O   PHE D  25 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER D  30 " --> pdb=" O   PHE D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 64
      removed outlier: 3.592A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   HIS D  61 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ILE D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 82 through 108
    Processing helix  chain 'D' and resid 109 through 114
      removed outlier: 4.287A  pdb=" N   GLY D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 149
      removed outlier: 3.684A  pdb=" N   THR D 132 " --> pdb=" O   GLY D 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU D 141 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 154
      removed outlier: 3.581A  pdb=" N   GLY D 154 " --> pdb=" O   GLU D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.759A  pdb=" N   LEU D 174 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   HIS D 177 " --> pdb=" O   LEU D 173 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 196
      Proline residue:  D 191  - end of helix
      removed outlier: 3.796A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 222
      Proline residue:  D 208  - end of helix
    Processing helix  chain 'D' and resid 229 through 238

    512 hydrogen bonds defined for protein.
    1524 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: 0.88

  Time building geometry restraints manager: 0.56 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: 1212
        1.32 -     1.44: 1844
        1.44 -     1.57: 4092
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 7180
  Sorted by residual:
  bond pdb=" CE1 HIS D 105 "
       pdb=" NE2 HIS D 105 "
    ideal  model  delta    sigma   weight residual
    1.321  1.373 -0.052 1.00e-02 1.00e+04 2.69e+01
  bond pdb=" CE1 HIS C 105 "
       pdb=" NE2 HIS C 105 "
    ideal  model  delta    sigma   weight residual
    1.321  1.373 -0.052 1.00e-02 1.00e+04 2.69e+01
  bond pdb=" CE1 HIS A 105 "
       pdb=" NE2 HIS A 105 "
    ideal  model  delta    sigma   weight residual
    1.321  1.373 -0.052 1.00e-02 1.00e+04 2.69e+01
  bond pdb=" CE1 HIS B 105 "
       pdb=" NE2 HIS B 105 "
    ideal  model  delta    sigma   weight residual
    1.321  1.373 -0.052 1.00e-02 1.00e+04 2.69e+01
  bond pdb=" CE1 HIS A 201 "
       pdb=" NE2 HIS A 201 "
    ideal  model  delta    sigma   weight residual
    1.321  1.368 -0.047 1.00e-02 1.00e+04 2.22e+01
  ... (remaining 7175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 7844
        1.02 -     2.04: 1696
        2.04 -     3.06: 220
        3.06 -     4.08: 52
        4.08 -     5.09: 8
  Bond angle restraints: 9820
  Sorted by residual:
  angle pdb=" NE  ARG A  11 "
        pdb=" CZ  ARG A  11 "
        pdb=" NH1 ARG A  11 "
      ideal   model   delta    sigma   weight residual
     121.50  119.15    2.35 1.00e+00 1.00e+00 5.51e+00
  angle pdb=" NE  ARG B  11 "
        pdb=" CZ  ARG B  11 "
        pdb=" NH1 ARG B  11 "
      ideal   model   delta    sigma   weight residual
     121.50  119.15    2.35 1.00e+00 1.00e+00 5.51e+00
  angle pdb=" NE  ARG D  11 "
        pdb=" CZ  ARG D  11 "
        pdb=" NH1 ARG D  11 "
      ideal   model   delta    sigma   weight residual
     121.50  119.15    2.35 1.00e+00 1.00e+00 5.51e+00
  angle pdb=" NE  ARG C  11 "
        pdb=" CZ  ARG C  11 "
        pdb=" NH1 ARG C  11 "
      ideal   model   delta    sigma   weight residual
     121.50  119.15    2.35 1.00e+00 1.00e+00 5.51e+00
  angle pdb=" CA  VAL A  83 "
        pdb=" CB  VAL A  83 "
        pdb=" CG1 VAL A  83 "
      ideal   model   delta    sigma   weight residual
     110.40  114.23   -3.83 1.70e+00 3.46e-01 5.08e+00
  ... (remaining 9815 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3800
       17.90 -    35.80: 264
       35.80 -    53.70: 60
       53.70 -    71.60: 4
       71.60 -    89.49: 4
  Dihedral angle restraints: 4132
    sinusoidal: 1436
      harmonic: 2696
  Sorted by residual:
  dihedral pdb=" CA  GLU C 155 "
           pdb=" CB  GLU C 155 "
           pdb=" CG  GLU C 155 "
           pdb=" CD  GLU C 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.21   50.21     3      1.50e+01 4.44e-03 8.87e+00
  dihedral pdb=" CA  GLU D 155 "
           pdb=" CB  GLU D 155 "
           pdb=" CG  GLU D 155 "
           pdb=" CD  GLU D 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.21   50.21     3      1.50e+01 4.44e-03 8.87e+00
  dihedral pdb=" CA  GLU A 155 "
           pdb=" CB  GLU A 155 "
           pdb=" CG  GLU A 155 "
           pdb=" CD  GLU A 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.21   50.21     3      1.50e+01 4.44e-03 8.87e+00
  ... (remaining 4129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 676
       0.048 -    0.095: 360
       0.095 -    0.143: 100
       0.143 -    0.191: 52
       0.191 -    0.239: 12
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CB  VAL C  83 "
            pdb=" CA  VAL C  83 "
            pdb=" CG1 VAL C  83 "
            pdb=" CG2 VAL C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL D  83 "
            pdb=" CA  VAL D  83 "
            pdb=" CG1 VAL D  83 "
            pdb=" CG2 VAL D  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL B  83 "
            pdb=" CA  VAL B  83 "
            pdb=" CG1 VAL B  83 "
            pdb=" CG2 VAL B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 136 "    0.037 2.00e-02 2.50e+03   2.44e-02 1.04e+01
        pdb=" CG  PHE C 136 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 136 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 136 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 136 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 136 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 136 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 136 "   -0.037 2.00e-02 2.50e+03   2.44e-02 1.04e+01
        pdb=" CG  PHE B 136 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 136 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 136 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 136 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 136 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 136 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 136 "   -0.037 2.00e-02 2.50e+03   2.44e-02 1.04e+01
        pdb=" CG  PHE A 136 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 136 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 136 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 136 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 136 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 136 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2684
        2.89 -     3.39: 7480
        3.39 -     3.90: 12704
        3.90 -     4.40: 15012
        4.40 -     4.90: 25248
  Nonbonded interactions: 63128
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 182 "
            pdb=" OG  SER D 188 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" OG  SER B 182 "
            pdb=" OG  SER B 188 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" OG  SER C 182 "
            pdb=" OG  SER C 188 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" OG  SER A 182 "
            pdb=" OG  SER A 188 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" ND2 ASN A 123 "
            pdb=" O   HIS A 177 "
     model   vdw
     2.410 3.120
  ... (remaining 63123 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             0.040
  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:          0.060
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.570
  Find NCS groups from input model:        0.030
  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:7.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
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      :  0.010   0.052   7180  Z= 0.632
  Angle     :  0.872   5.095   9820  Z= 0.566
  Chirality :  0.068   0.239   1200
  Planarity :  0.007   0.032   1236
  Dihedral  : 13.225  89.494   2404
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  5.00 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.60 (0.23), residues: 948
  helix: -1.67 (0.15), residues: 616
  sheet:  None (None), residues: 0
  loop : -1.48 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.004   ARG C  11 
 TYR   0.012   0.004   TYR B 221 
 PHE   0.038   0.009   PHE C  14 
 TRP   0.039   0.008   TRP B  34 
 HIS   0.006   0.002   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00979 ( 7180)
  covalent geometry    : angle       0.87186 ( 9820)
  hydrogen bonds       : bond        0.23582 (  512)
  hydrogen bonds       : angle       9.68771 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7005 (mt-10)
REVERT: B  106 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7004 (mt-10)
REVERT: C  106 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7004 (mt-10)
REVERT: D  106 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7003 (mt-10)
  outliers start: 20
  outliers final: 12
  residues processed: 68
  average time/residue: 0.2395
  time to fit residues: 17.8780
Evaluate side-chains
  56 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  122 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 119 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 = 0.3518 r_free = 0.3518 target = 0.139402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.115640 restraints weight = 7518.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.76
r_work: 0.3130 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
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   0.026   7180  Z= 0.131
  Angle     :  0.509   5.303   9820  Z= 0.262
  Chirality :  0.037   0.117   1200
  Planarity :  0.005   0.035   1236
  Dihedral  :  3.942  19.364   1008
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.37 (0.27), residues: 948
  helix:  0.83 (0.18), residues: 656
  sheet:  None (None), residues: 0
  loop : -0.98 (0.41), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.005   0.001   TYR B 219 
 PHE   0.010   0.001   PHE B  48 
 TRP   0.002   0.001   TRP B 205 
 HIS   0.003   0.001   HIS D 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7180)
  covalent geometry    : angle       0.50869 ( 9820)
  hydrogen bonds       : bond        0.03840 (  512)
  hydrogen bonds       : angle       5.35978 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6893 (mt-10)
REVERT: B  106 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6902 (mt-10)
REVERT: C  106 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6908 (mt-10)
REVERT: D  106 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6917 (mt-10)
  outliers start: 8
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2648
  time to fit residues: 17.4444
Evaluate side-chains
  44 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
A 129 GLN
B  33 ASN
B 129 GLN
C  33 ASN
C 129 GLN
D  33 ASN
D 129 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.132893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.108771 restraints weight = 7506.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.72
r_work: 0.3046 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7180  Z= 0.230
  Angle     :  0.572   5.243   9820  Z= 0.288
  Chirality :  0.041   0.129   1200
  Planarity :  0.005   0.040   1236
  Dihedral  :  4.041  17.222    996
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  6.11 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.27), residues: 948
  helix:  1.06 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.62 (0.43), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 187 
 TYR   0.005   0.002   TYR A  89 
 PHE   0.015   0.002   PHE D  14 
 TRP   0.004   0.001   TRP B 205 
 HIS   0.005   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 7180)
  covalent geometry    : angle       0.57231 ( 9820)
  hydrogen bonds       : bond        0.04039 (  512)
  hydrogen bonds       : angle       5.37692 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7735 (mm-30) cc_final: 0.6985 (mt-10)
REVERT: A  218 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7377 (mt)
REVERT: B  106 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6987 (mt-10)
REVERT: B  218 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7374 (mt)
REVERT: C  106 GLU cc_start: 0.7740 (mm-30) cc_final: 0.6985 (mt-10)
REVERT: C  218 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (mt)
REVERT: D  106 GLU cc_start: 0.7742 (mm-30) cc_final: 0.6986 (mt-10)
REVERT: D  218 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7374 (mt)
  outliers start: 8
  outliers final: 0
  residues processed: 44
  average time/residue: 0.3935
  time to fit residues: 18.7989
Evaluate side-chains
  40 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain D residue  218 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.136903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.112473 restraints weight = 7465.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.79
r_work: 0.3094 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7180  Z= 0.126
  Angle     :  0.489   5.077   9820  Z= 0.249
  Chirality :  0.037   0.119   1200
  Planarity :  0.004   0.038   1236
  Dihedral  :  3.791  15.758    996
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.49 (0.28), residues: 948
  helix:  1.58 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.34 (0.45), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 187 
 TYR   0.005   0.001   TYR B 219 
 PHE   0.008   0.001   PHE D 136 
 TRP   0.002   0.001   TRP B  34 
 HIS   0.002   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7180)
  covalent geometry    : angle       0.48895 ( 9820)
  hydrogen bonds       : bond        0.03373 (  512)
  hydrogen bonds       : angle       4.99278 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7743 (mm-30) cc_final: 0.6961 (mt-10)
REVERT: B  106 GLU cc_start: 0.7763 (mm-30) cc_final: 0.6977 (mt-10)
REVERT: C  106 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6978 (mt-10)
REVERT: D  106 GLU cc_start: 0.7762 (mm-30) cc_final: 0.6979 (mt-10)
  outliers start: 8
  outliers final: 0
  residues processed: 48
  average time/residue: 0.3792
  time to fit residues: 19.8349
Evaluate side-chains
  40 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 6 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0010
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.8992

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 119 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 = 0.3500 r_free = 0.3500 target = 0.137794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.113372 restraints weight = 7476.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.81
r_work: 0.3105 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7180  Z= 0.116
  Angle     :  0.479   5.051   9820  Z= 0.242
  Chirality :  0.037   0.117   1200
  Planarity :  0.004   0.036   1236
  Dihedral  :  3.689  15.246    996
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.78 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.83 (0.29), residues: 948
  helix:  1.84 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.21 (0.46), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.004   0.001   TYR D 219 
 PHE   0.008   0.001   PHE A  25 
 TRP   0.002   0.000   TRP A  34 
 HIS   0.002   0.001   HIS D 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7180)
  covalent geometry    : angle       0.47861 ( 9820)
  hydrogen bonds       : bond        0.03262 (  512)
  hydrogen bonds       : angle       4.85883 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7742 (mm-30) cc_final: 0.6968 (mt-10)
REVERT: B  106 GLU cc_start: 0.7762 (mm-30) cc_final: 0.6986 (mt-10)
REVERT: C  106 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6971 (mt-10)
REVERT: D  106 GLU cc_start: 0.7758 (mm-30) cc_final: 0.6982 (mt-10)
  outliers start: 8
  outliers final: 0
  residues processed: 52
  average time/residue: 0.3624
  time to fit residues: 20.5702
Evaluate side-chains
  44 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 119 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 = 0.3556 r_free = 0.3556 target = 0.142431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.118233 restraints weight = 7412.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.79
r_work: 0.3174 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   7180  Z= 0.090
  Angle     :  0.452   4.958   9820  Z= 0.229
  Chirality :  0.036   0.112   1200
  Planarity :  0.004   0.035   1236
  Dihedral  :  3.502  14.877    996
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.33 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.11 (0.29), residues: 948
  helix:  2.08 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.22 (0.47), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 187 
 TYR   0.004   0.001   TYR B 219 
 PHE   0.007   0.001   PHE C  17 
 TRP   0.002   0.000   TRP A 202 
 HIS   0.002   0.000   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 ( 7180)
  covalent geometry    : angle       0.45203 ( 9820)
  hydrogen bonds       : bond        0.02959 (  512)
  hydrogen bonds       : angle       4.68119 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7052 (mt-10)
REVERT: B  106 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7066 (mt-10)
REVERT: C  106 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7034 (mt-10)
REVERT: D  106 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7038 (mt-10)
  outliers start: 4
  outliers final: 0
  residues processed: 48
  average time/residue: 0.3955
  time to fit residues: 20.6520
Evaluate side-chains
  44 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0370
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    3.6066

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.135042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.110469 restraints weight = 7520.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.80
r_work: 0.3062 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7180  Z= 0.169
  Angle     :  0.520   5.144   9820  Z= 0.261
  Chirality :  0.039   0.123   1200
  Planarity :  0.004   0.034   1236
  Dihedral  :  3.822  16.739    996
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.85 (0.29), residues: 948
  helix:  1.81 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.10 (0.47), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  11 
 TYR   0.005   0.001   TYR D 219 
 PHE   0.011   0.002   PHE A  14 
 TRP   0.003   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 7180)
  covalent geometry    : angle       0.52012 ( 9820)
  hydrogen bonds       : bond        0.03571 (  512)
  hydrogen bonds       : angle       4.94089 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  106 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7602 (mm-30)
REVERT: B  106 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7608 (mm-30)
REVERT: C  106 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: D  106 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7605 (mm-30)
  outliers start: 8
  outliers final: 0
  residues processed: 48
  average time/residue: 0.3531
  time to fit residues: 18.4041
Evaluate side-chains
  40 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.133870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.109177 restraints weight = 7617.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.82
r_work: 0.3044 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7180  Z= 0.194
  Angle     :  0.535   5.185   9820  Z= 0.268
  Chirality :  0.040   0.126   1200
  Planarity :  0.004   0.035   1236
  Dihedral  :  3.947  17.108    996
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.33 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.62 (0.29), residues: 948
  helix:  1.62 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.13 (0.47), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  11 
 TYR   0.005   0.001   TYR D 219 
 PHE   0.011   0.002   PHE D  14 
 TRP   0.003   0.001   TRP D 205 
 HIS   0.004   0.001   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7180)
  covalent geometry    : angle       0.53508 ( 9820)
  hydrogen bonds       : bond        0.03676 (  512)
  hydrogen bonds       : angle       5.07314 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.157 
Fit side-chains
REVERT: C  106 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7659 (mm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 40
  average time/residue: 0.4230
  time to fit residues: 18.0858
Evaluate side-chains
  36 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 61 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.134580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.109890 restraints weight = 7494.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.81
r_work: 0.3054 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7180  Z= 0.173
  Angle     :  0.520   5.169   9820  Z= 0.261
  Chirality :  0.039   0.125   1200
  Planarity :  0.004   0.035   1236
  Dihedral  :  3.901  16.906    996
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.33 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.64 (0.29), residues: 948
  helix:  1.65 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.15 (0.47), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C  11 
 TYR   0.005   0.001   TYR D 219 
 PHE   0.010   0.001   PHE B 136 
 TRP   0.003   0.001   TRP C 205 
 HIS   0.004   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 7180)
  covalent geometry    : angle       0.51979 ( 9820)
  hydrogen bonds       : bond        0.03557 (  512)
  hydrogen bonds       : angle       5.00293 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.217 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 40
  average time/residue: 0.4495
  time to fit residues: 19.4582
Evaluate side-chains
  36 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.9590

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.141238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.116621 restraints weight = 7317.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.79
r_work: 0.3146 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7180  Z= 0.094
  Angle     :  0.462   4.946   9820  Z= 0.234
  Chirality :  0.036   0.113   1200
  Planarity :  0.004   0.037   1236
  Dihedral  :  3.606  14.904    996
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.33 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.20 (0.29), residues: 948
  helix:  2.19 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.08 (0.45), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 152 
 TYR   0.004   0.001   TYR D 219 
 PHE   0.008   0.001   PHE C  25 
 TRP   0.004   0.001   TRP C 202 
 HIS   0.001   0.000   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 7180)
  covalent geometry    : angle       0.46151 ( 9820)
  hydrogen bonds       : bond        0.03013 (  512)
  hydrogen bonds       : angle       4.72087 ( 1524)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.188 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 48
  average time/residue: 0.3130
  time to fit residues: 16.3708
Evaluate side-chains
  44 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.133194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.108709 restraints weight = 7578.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.75
r_work: 0.3037 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7180  Z= 0.219
  Angle     :  0.555   5.217   9820  Z= 0.277
  Chirality :  0.041   0.130   1200
  Planarity :  0.004   0.035   1236
  Dihedral  :  3.969  17.947    996
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.66 (0.28), residues: 948
  helix:  1.70 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.25 (0.46), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  85 
 TYR   0.005   0.001   TYR D  89 
 PHE   0.013   0.002   PHE C  14 
 TRP   0.004   0.001   TRP C 205 
 HIS   0.004   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 7180)
  covalent geometry    : angle       0.55487 ( 9820)
  hydrogen bonds       : bond        0.03778 (  512)
  hydrogen bonds       : angle       5.09383 ( 1524)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1534.95 seconds
wall clock time: 27 minutes 10.47 seconds (1630.47 seconds total)