Starting phenix.real_space_refine
on Tue Mar  3 17:15:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2026/7ubb_26437.map"
  }
  resolution = 4.5
  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=   0.000 sd=   0.026
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    4816      2.51       5
     N    1256      2.21       5
     O    1352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7448
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 931
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 111}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    D, E, F, G, H, I, J
  Time building chain proxies: 0.86, per 1000 atoms: 0.12
  Number of scatterers: 7448
  At special positions: 0
  Unit cell: (96.193, 92.597, 151.032, 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    1352      8.00
     N    1256      7.00
     C    4816      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: 0.66
  Conformation dependent library (CDL) restraints added in 264.3 milliseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 16 sheets defined
      40.3% alpha, 25.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'C' and resid 110 through 121
      removed outlier: 3.662A  pdb=" N   GLY C 121 " --> pdb=" O   ALA C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 189
    Processing helix  chain 'C' and resid 193 through 199
      removed outlier: 4.055A  pdb=" N   LYS C 197 " --> pdb=" O   ASP C 193 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LYS C 198 " --> pdb=" O   PHE C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP C 216 " --> pdb=" O   MET C 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 121
      removed outlier: 3.662A  pdb=" N   GLY D 121 " --> pdb=" O   ALA D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 189
    Processing helix  chain 'D' and resid 193 through 199
      removed outlier: 4.054A  pdb=" N   LYS D 197 " --> pdb=" O   ASP D 193 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS D 198 " --> pdb=" O   PHE D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP D 216 " --> pdb=" O   MET D 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 121
      removed outlier: 3.663A  pdb=" N   GLY E 121 " --> pdb=" O   ALA E 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 189
    Processing helix  chain 'E' and resid 193 through 199
      removed outlier: 4.054A  pdb=" N   LYS E 197 " --> pdb=" O   ASP E 193 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS E 198 " --> pdb=" O   PHE E 194 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 216
      removed outlier: 3.596A  pdb=" N   TRP E 216 " --> pdb=" O   MET E 212 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 121
      removed outlier: 3.662A  pdb=" N   GLY F 121 " --> pdb=" O   ALA F 117 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 189
    Processing helix  chain 'F' and resid 193 through 199
      removed outlier: 4.055A  pdb=" N   LYS F 197 " --> pdb=" O   ASP F 193 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS F 198 " --> pdb=" O   PHE F 194 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP F 216 " --> pdb=" O   MET F 212 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 111 through 121
      removed outlier: 3.661A  pdb=" N   GLY G 121 " --> pdb=" O   ALA G 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 179 through 189
    Processing helix  chain 'G' and resid 193 through 199
      removed outlier: 4.054A  pdb=" N   LYS G 197 " --> pdb=" O   ASP G 193 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS G 198 " --> pdb=" O   PHE G 194 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 201 through 216
      removed outlier: 3.596A  pdb=" N   TRP G 216 " --> pdb=" O   MET G 212 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 111 through 121
      removed outlier: 3.661A  pdb=" N   GLY H 121 " --> pdb=" O   ALA H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 179 through 189
    Processing helix  chain 'H' and resid 193 through 199
      removed outlier: 4.054A  pdb=" N   LYS H 197 " --> pdb=" O   ASP H 193 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS H 198 " --> pdb=" O   PHE H 194 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP H 216 " --> pdb=" O   MET H 212 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 111 through 121
      removed outlier: 3.661A  pdb=" N   GLY I 121 " --> pdb=" O   ALA I 117 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 179 through 189
    Processing helix  chain 'I' and resid 193 through 199
      removed outlier: 4.055A  pdb=" N   LYS I 197 " --> pdb=" O   ASP I 193 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LYS I 198 " --> pdb=" O   PHE I 194 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP I 216 " --> pdb=" O   MET I 212 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 111 through 121
      removed outlier: 3.662A  pdb=" N   GLY J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 179 through 189
    Processing helix  chain 'J' and resid 193 through 199
      removed outlier: 4.054A  pdb=" N   LYS J 197 " --> pdb=" O   ASP J 193 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS J 198 " --> pdb=" O   PHE J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 201 through 216
      removed outlier: 3.595A  pdb=" N   TRP J 216 " --> pdb=" O   MET J 212 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 123 through 132
    Processing sheet with id=AA2, first strand: chain 'C' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU C 147 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 123 through 132
    Processing sheet with id=AA4, first strand: chain 'D' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU D 147 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 132
    Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU E 147 " --> pdb=" O   LEU E 137 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 123 through 132
    Processing sheet with id=AA8, first strand: chain 'F' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU F 147 " --> pdb=" O   LEU F 137 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 123 through 132
    Processing sheet with id=AB1, first strand: chain 'G' and resid 136 through 139
      removed outlier: 7.168A  pdb=" N   GLU G 147 " --> pdb=" O   LEU G 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 132
    Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU H 147 " --> pdb=" O   LEU H 137 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 123 through 132
    Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU I 147 " --> pdb=" O   LEU I 137 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'J' and resid 123 through 132
    Processing sheet with id=AB7, first strand: chain 'J' and resid 136 through 139
      removed outlier: 7.167A  pdb=" N   GLU J 147 " --> pdb=" O   LEU J 137 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    963 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: 0.97

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2304
        1.35 -     1.46: 1883
        1.46 -     1.58: 3373
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7600
  Sorted by residual:
  bond pdb=" CA  ASP G 151 "
       pdb=" CB  ASP G 151 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 8.08e-01
  bond pdb=" CA  ASP D 151 "
       pdb=" CB  ASP D 151 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.81e-01
  bond pdb=" CA  ASP J 151 "
       pdb=" CB  ASP J 151 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.80e-01
  bond pdb=" CA  ASP H 151 "
       pdb=" CB  ASP H 151 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.76e-01
  bond pdb=" CA  ASP C 151 "
       pdb=" CB  ASP C 151 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.60e-01
  ... (remaining 7595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 9707
        1.39 -     2.79: 372
        2.79 -     4.18: 89
        4.18 -     5.57: 16
        5.57 -     6.97: 16
  Bond angle restraints: 10200
  Sorted by residual:
  angle pdb=" C   LEU H 150 "
        pdb=" N   ASP H 151 "
        pdb=" CA  ASP H 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" C   LEU F 150 "
        pdb=" N   ASP F 151 "
        pdb=" CA  ASP F 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.69   -6.15 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" C   LEU I 150 "
        pdb=" N   ASP I 151 "
        pdb=" CA  ASP I 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   LEU D 150 "
        pdb=" N   ASP D 151 "
        pdb=" CA  ASP D 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.65   -6.11 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" C   LEU G 150 "
        pdb=" N   ASP G 151 "
        pdb=" CA  ASP G 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.65   -6.11 1.91e+00 2.74e-01 1.02e+01
  ... (remaining 10195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.08: 3696
       12.08 -    24.17: 528
       24.17 -    36.25: 200
       36.25 -    48.33: 40
       48.33 -    60.42: 40
  Dihedral angle restraints: 4504
    sinusoidal: 1896
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" CA  SER H 214 "
           pdb=" C   SER H 214 "
           pdb=" N   LYS H 215 "
           pdb=" CA  LYS H 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.06  -16.94     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  SER C 214 "
           pdb=" C   SER C 214 "
           pdb=" N   LYS C 215 "
           pdb=" CA  LYS C 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  SER J 214 "
           pdb=" C   SER J 214 "
           pdb=" N   LYS J 215 "
           pdb=" CA  LYS J 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 4501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 589
       0.030 -    0.060: 301
       0.060 -    0.091: 144
       0.091 -    0.121: 38
       0.121 -    0.151: 8
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  ASP I 151 "
            pdb=" N   ASP I 151 "
            pdb=" C   ASP I 151 "
            pdb=" CB  ASP I 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ASP D 151 "
            pdb=" N   ASP D 151 "
            pdb=" C   ASP D 151 "
            pdb=" CB  ASP D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ASP H 151 "
            pdb=" N   ASP H 151 "
            pdb=" C   ASP H 151 "
            pdb=" CB  ASP H 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1248
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 216 "   -0.010 2.00e-02 2.50e+03   1.00e-02 2.52e+00
        pdb=" CG  TRP F 216 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 216 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 216 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 216 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 216 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 216 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 216 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 216 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 216 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP I 216 "    0.010 2.00e-02 2.50e+03   9.93e-03 2.46e+00
        pdb=" CG  TRP I 216 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP I 216 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP I 216 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP I 216 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP I 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP I 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP I 216 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP I 216 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP I 216 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G 216 "    0.010 2.00e-02 2.50e+03   9.91e-03 2.46e+00
        pdb=" CG  TRP G 216 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP G 216 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP G 216 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP G 216 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP G 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP G 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G 216 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP G 216 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1245 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1212
        2.77 -     3.30: 7163
        3.30 -     3.83: 11913
        3.83 -     4.37: 12490
        4.37 -     4.90: 21741
  Nonbonded interactions: 54519
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN C 127 "
            pdb=" OE2 GLU D 144 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" ND2 ASN H 127 "
            pdb=" OE2 GLU I 144 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   LYS F 186 "
            pdb=" OG  SER F 190 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LYS E 186 "
            pdb=" OG  SER E 190 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LYS J 186 "
            pdb=" OG  SER J 190 "
     model   vdw
     2.299 3.040
  ... (remaining 54514 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}
Set refine NCS operators
  NCS operators will be refined.
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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.190
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5995
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      :  0.002   0.022   7600  Z= 0.122
  Angle     :  0.684   6.967  10200  Z= 0.355
  Chirality :  0.043   0.151   1080
  Planarity :  0.002   0.010   1248
  Dihedral  : 14.316  60.416   2840
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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 are not related in a simple way.
  whole: -1.04 (0.26), residues: 880
  helix:  1.14 (0.29), residues: 280
  sheet:  0.11 (0.33), residues: 272
  loop : -3.15 (0.23), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 132 
 TYR   0.008   0.001   TYR I 110 
 PHE   0.004   0.001   PHE C 194 
 TRP   0.026   0.002   TRP F 216 
 HIS   0.001   0.001   HIS F 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7600)
  covalent geometry    : angle       0.68431 (10200)
  hydrogen bonds       : bond        0.07258 (  321)
  hydrogen bonds       : angle       4.61324 (  963)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.043 
Fit side-chains
REVERT: C  135 GLU cc_start: 0.8466 (tp30) cc_final: 0.5309 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0984
  time to fit residues: 2.0079
Evaluate side-chains
  9 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.4980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
F 122 GLN
F 153 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.201869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.152498 restraints weight = 1366.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.161458 restraints weight = 846.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.167922 restraints weight = 557.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.172349 restraints weight = 394.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.175959 restraints weight = 301.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5445
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7600  Z= 0.096
  Angle     :  0.536   5.917  10200  Z= 0.286
  Chirality :  0.044   0.150   1080
  Planarity :  0.002   0.010   1248
  Dihedral  :  3.657  12.714    984
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  5.05 %
    Favored  : 93.94 %
  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 are not related in a simple way.
  whole: -1.00 (0.27), residues: 880
  helix:  1.07 (0.30), residues: 288
  sheet:  0.22 (0.33), residues: 272
  loop : -3.22 (0.23), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 132 
 TYR   0.004   0.001   TYR F 110 
 PHE   0.004   0.001   PHE I 194 
 TRP   0.012   0.001   TRP E 216 
 HIS   0.001   0.001   HIS J 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 7600)
  covalent geometry    : angle       0.53553 (10200)
  hydrogen bonds       : bond        0.02869 (  321)
  hydrogen bonds       : angle       3.95642 (  963)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.037 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0771
  time to fit residues: 3.1977
Evaluate side-chains
  28 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.0010
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0060
   chunk 51 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0050
   chunk 71 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3216
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.187090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.134699 restraints weight = 1323.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.139600 restraints weight = 981.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.143404 restraints weight = 776.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.147030 restraints weight = 644.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.149532 restraints weight = 551.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5425
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7600  Z= 0.095
  Angle     :  0.529   5.727  10200  Z= 0.285
  Chirality :  0.044   0.145   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  3.637  11.040    984
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.27), residues: 880
  helix:  0.60 (0.30), residues: 288
  sheet:  0.17 (0.32), residues: 272
  loop : -3.48 (0.24), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 132 
 TYR   0.004   0.000   TYR I 110 
 PHE   0.007   0.001   PHE G 165 
 TRP   0.014   0.001   TRP E 216 
 HIS   0.001   0.001   HIS I 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 7600)
  covalent geometry    : angle       0.52881 (10200)
  hydrogen bonds       : bond        0.02947 (  321)
  hydrogen bonds       : angle       4.05470 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8523 (m-80) cc_final: 0.7886 (m-80)
REVERT: E  171 PHE cc_start: 0.7914 (t80) cc_final: 0.7053 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0794
  time to fit residues: 3.7938
Evaluate side-chains
  37 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 86 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0370
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8142
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.193212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.143950 restraints weight = 1327.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.148138 restraints weight = 1019.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.151554 restraints weight = 824.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.154401 restraints weight = 693.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.156788 restraints weight = 599.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5377
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7600  Z= 0.105
  Angle     :  0.546   5.381  10200  Z= 0.296
  Chirality :  0.043   0.141   1080
  Planarity :  0.002   0.014   1248
  Dihedral  :  3.945  11.528    984
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  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 are not related in a simple way.
  whole: -1.54 (0.26), residues: 880
  helix:  0.40 (0.29), residues: 280
  sheet: -0.11 (0.32), residues: 272
  loop : -3.17 (0.24), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 119 
 TYR   0.003   0.001   TYR J 123 
 PHE   0.008   0.001   PHE H 165 
 TRP   0.021   0.002   TRP J 216 
 HIS   0.002   0.001   HIS G 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7600)
  covalent geometry    : angle       0.54552 (10200)
  hydrogen bonds       : bond        0.03253 (  321)
  hydrogen bonds       : angle       4.70751 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.040 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8504 (m-80) cc_final: 0.7858 (m-80)
REVERT: E  171 PHE cc_start: 0.8038 (t80) cc_final: 0.7062 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0736
  time to fit residues: 3.4450
Evaluate side-chains
  35 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0030
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0870
   chunk 68 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0010
   overall best weight:    0.3574
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 185 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.195640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.140823 restraints weight = 1287.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.146332 restraints weight = 932.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.151010 restraints weight = 722.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.154564 restraints weight = 586.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.156977 restraints weight = 494.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5389
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   7600  Z= 0.103
  Angle     :  0.588   5.398  10200  Z= 0.321
  Chirality :  0.045   0.136   1080
  Planarity :  0.002   0.013   1248
  Dihedral  :  4.439  19.419    984
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  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 are not related in a simple way.
  whole: -2.13 (0.24), residues: 880
  helix:  0.47 (0.30), residues: 280
  sheet: -0.80 (0.33), residues: 192
  loop : -3.20 (0.20), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 119 
 TYR   0.004   0.001   TYR D 110 
 PHE   0.005   0.001   PHE D 194 
 TRP   0.028   0.003   TRP E 196 
 HIS   0.001   0.001   HIS F 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 7600)
  covalent geometry    : angle       0.58844 (10200)
  hydrogen bonds       : bond        0.03289 (  321)
  hydrogen bonds       : angle       4.70016 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.039 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8504 (m-80) cc_final: 0.7875 (m-80)
REVERT: E  135 GLU cc_start: 0.8590 (pt0) cc_final: 0.8160 (mp0)
REVERT: E  162 CYS cc_start: 0.9309 (p) cc_final: 0.9058 (p)
REVERT: E  171 PHE cc_start: 0.7972 (t80) cc_final: 0.6937 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0697
  time to fit residues: 3.0758
Evaluate side-chains
  37 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0770
   chunk 57 optimal weight:    0.0170
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7978
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 185 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.197203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.141606 restraints weight = 1151.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.147217 restraints weight = 846.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.152022 restraints weight = 663.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.155925 restraints weight = 540.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.158747 restraints weight = 454.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5466
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   7600  Z= 0.097
  Angle     :  0.624   9.771  10200  Z= 0.317
  Chirality :  0.044   0.131   1080
  Planarity :  0.002   0.012   1248
  Dihedral  :  4.416  20.580    984
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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 are not related in a simple way.
  whole: -1.82 (0.26), residues: 880
  helix:  0.54 (0.30), residues: 280
  sheet: -0.79 (0.31), residues: 272
  loop : -3.15 (0.24), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 119 
 TYR   0.003   0.001   TYR F 110 
 PHE   0.013   0.001   PHE C 165 
 TRP   0.026   0.003   TRP E 196 
 HIS   0.001   0.000   HIS J 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 7600)
  covalent geometry    : angle       0.62359 (10200)
  hydrogen bonds       : bond        0.03274 (  321)
  hydrogen bonds       : angle       4.81785 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.037 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8507 (m-80) cc_final: 0.7846 (m-80)
REVERT: E  173 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7986 (mmtm)
REVERT: E  174 THR cc_start: 0.8110 (p) cc_final: 0.7548 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0753
  time to fit residues: 3.2983
Evaluate side-chains
  37 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0570
   chunk 55 optimal weight:    5.9990
   chunk 12 optimal weight:    0.1980
   chunk 46 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0470
   chunk 15 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:   20.0000
   overall best weight:    0.2796
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.197503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.136530 restraints weight = 1201.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.142521 restraints weight = 868.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.147494 restraints weight = 679.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.150769 restraints weight = 553.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.154644 restraints weight = 475.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5312
moved from start:          0.6148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   7600  Z= 0.101
  Angle     :  0.611   7.955  10200  Z= 0.317
  Chirality :  0.044   0.133   1080
  Planarity :  0.002   0.015   1248
  Dihedral  :  4.304  21.303    984
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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 are not related in a simple way.
  whole: -2.05 (0.26), residues: 880
  helix:  0.27 (0.30), residues: 280
  sheet: -0.73 (0.32), residues: 272
  loop : -3.41 (0.22), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 119 
 TYR   0.004   0.001   TYR D 110 
 PHE   0.008   0.001   PHE H 165 
 TRP   0.027   0.003   TRP E 196 
 HIS   0.001   0.000   HIS F 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 7600)
  covalent geometry    : angle       0.61138 (10200)
  hydrogen bonds       : bond        0.03360 (  321)
  hydrogen bonds       : angle       4.60836 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8538 (m-80) cc_final: 0.7877 (m-80)
REVERT: E  162 CYS cc_start: 0.9284 (p) cc_final: 0.9065 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0660
  time to fit residues: 2.9082
Evaluate side-chains
  38 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0170
   chunk 33 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    0.6422
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.193916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.133755 restraints weight = 1197.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.138889 restraints weight = 878.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.143975 restraints weight = 693.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.147435 restraints weight = 572.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.150664 restraints weight = 491.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5402
moved from start:          0.6454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7600  Z= 0.094
  Angle     :  0.572   6.414  10200  Z= 0.298
  Chirality :  0.042   0.132   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  3.733  10.861    984
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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 are not related in a simple way.
  whole: -1.95 (0.26), residues: 880
  helix:  0.22 (0.30), residues: 280
  sheet: -0.52 (0.31), residues: 272
  loop : -3.37 (0.23), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 119 
 TYR   0.003   0.001   TYR D 164 
 PHE   0.005   0.001   PHE H 165 
 TRP   0.028   0.003   TRP E 196 
 HIS   0.001   0.000   HIS F 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 7600)
  covalent geometry    : angle       0.57164 (10200)
  hydrogen bonds       : bond        0.03318 (  321)
  hydrogen bonds       : angle       4.66744 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8573 (m-80) cc_final: 0.7915 (m-80)
REVERT: E  173 LYS cc_start: 0.8107 (tmtt) cc_final: 0.7728 (mmtt)
REVERT: E  174 THR cc_start: 0.8094 (p) cc_final: 0.7490 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0678
  time to fit residues: 3.0579
Evaluate side-chains
  39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.9582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.193443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.134996 restraints weight = 1240.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.140889 restraints weight = 900.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.145556 restraints weight = 703.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.149285 restraints weight = 576.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.151498 restraints weight = 488.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5406
moved from start:          0.6582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7600  Z= 0.119
  Angle     :  0.652   6.083  10200  Z= 0.366
  Chirality :  0.043   0.139   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  3.884  12.431    984
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -1.98 (0.26), residues: 880
  helix:  0.10 (0.29), residues: 280
  sheet: -0.51 (0.32), residues: 272
  loop : -3.32 (0.23), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 119 
 TYR   0.005   0.001   TYR J 123 
 PHE   0.006   0.001   PHE C 165 
 TRP   0.030   0.002   TRP F 196 
 HIS   0.001   0.001   HIS F 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7600)
  covalent geometry    : angle       0.65231 (10200)
  hydrogen bonds       : bond        0.04342 (  321)
  hydrogen bonds       : angle       5.34636 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8597 (m-80) cc_final: 0.7922 (m-80)
REVERT: E  173 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7679 (mmtt)
REVERT: E  174 THR cc_start: 0.8163 (p) cc_final: 0.7403 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0718
  time to fit residues: 3.2412
Evaluate side-chains
  38 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 74 optimal weight:    0.1980
   chunk 60 optimal weight:    0.3980
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0030
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0870
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.2768
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.194458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.138219 restraints weight = 1224.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.143548 restraints weight = 905.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.147931 restraints weight = 721.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.152057 restraints weight = 597.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.154639 restraints weight = 504.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5430
moved from start:          0.6686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   7600  Z= 0.102
  Angle     :  0.626   6.155  10200  Z= 0.342
  Chirality :  0.045   0.161   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  3.733  10.887    984
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -2.02 (0.26), residues: 880
  helix:  0.05 (0.30), residues: 280
  sheet: -0.57 (0.33), residues: 272
  loop : -3.29 (0.23), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 119 
 TYR   0.004   0.001   TYR J 123 
 PHE   0.008   0.001   PHE H 165 
 TRP   0.030   0.002   TRP F 196 
 HIS   0.002   0.002   HIS J 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 7600)
  covalent geometry    : angle       0.62624 (10200)
  hydrogen bonds       : bond        0.03880 (  321)
  hydrogen bonds       : angle       5.11571 (  963)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.034 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8546 (m-80) cc_final: 0.7861 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0715
  time to fit residues: 3.0174
Evaluate side-chains
  35 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 5 optimal weight:    0.0050
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0770
   chunk 18 optimal weight:    0.7980
   chunk 83 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4952
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.194769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.136999 restraints weight = 1211.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.142361 restraints weight = 923.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.145993 restraints weight = 746.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.149601 restraints weight = 633.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.152557 restraints weight = 548.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5439
moved from start:          0.6736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7600  Z= 0.101
  Angle     :  0.625   5.622  10200  Z= 0.343
  Chirality :  0.044   0.138   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  4.014  11.809    984
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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 are not related in a simple way.
  whole: -1.85 (0.27), residues: 880
  helix:  0.29 (0.30), residues: 280
  sheet: -0.52 (0.33), residues: 272
  loop : -3.25 (0.24), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 119 
 TYR   0.004   0.000   TYR F 164 
 PHE   0.018   0.002   PHE C 165 
 TRP   0.028   0.002   TRP E 196 
 HIS   0.001   0.001   HIS G 185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 7600)
  covalent geometry    : angle       0.62491 (10200)
  hydrogen bonds       : bond        0.03949 (  321)
  hydrogen bonds       : angle       5.31584 (  963)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 904.35 seconds
wall clock time: 16 minutes 23.57 seconds (983.57 seconds total)