Starting phenix.real_space_refine
on Wed Mar 12 07:03:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_26437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_26437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_26437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_26437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ubb_26437/03_2025/7ubb_26437.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.026
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    E, D, G, F, I, H, J
  Time building chain proxies: 3.13, per 1000 atoms: 0.42
  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.81
  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: 1.84

  Time building geometry restraints manager: 2.04 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  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:             1.290
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     18.800
  Find NCS groups from input model:        0.150
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.610
-------------------------------------------------------------------------------
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= 0.149
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (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
 TRP   0.026   0.002   TRP F 216 
 HIS   0.001   0.001   HIS F 185 
 PHE   0.004   0.001   PHE C 194 
 TYR   0.008   0.001   TYR I 110 
 ARG   0.003   0.000   ARG F 132 

*********************** 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  : 0.107 
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: 0.2234
  time to fit residues: 4.5789
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.3980
   chunk 66 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0670
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0060
   overall best weight:    0.3334
-------------------------------------------------------------------------------
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 = 0.4511 r_free = 0.4511 target = 0.203646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.154544 restraints weight = 1327.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.162952 restraints weight = 822.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.169545 restraints weight = 547.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5439
moved from start:          0.2032

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= 0.121
  Angle     :  0.538   5.914  10200  Z= 0.287
  Chirality :  0.044   0.150   1080
  Planarity :  0.002   0.010   1248
  Dihedral  :  3.642  12.514    984
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.83
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.27), residues: 880
  helix:  1.03 (0.30), residues: 288
  sheet:  0.26 (0.33), residues: 272
  loop : -3.24 (0.23), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 216 
 HIS   0.000   0.000   HIS J 185 
 PHE   0.004   0.001   PHE D 165 
 TYR   0.004   0.001   TYR F 110 
 ARG   0.003   0.000   ARG G 132 

*********************** 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  : 0.116 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1730
  time to fit residues: 7.2245
Evaluate side-chains
  29 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0370
   chunk 27 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0670
   chunk 60 optimal weight:    0.0020
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.3204
-------------------------------------------------------------------------------
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 = 0.4545 r_free = 0.4545 target = 0.188941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.131941 restraints weight = 1319.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.137016 restraints weight = 999.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.141409 restraints weight = 800.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5372
moved from start:          0.2179

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= 0.127
  Angle     :  0.577   6.139  10200  Z= 0.296
  Chirality :  0.044   0.151   1080
  Planarity :  0.002   0.011   1248
  Dihedral  :  3.637  10.929    984
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.50
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.27), residues: 880
  helix:  0.63 (0.30), residues: 288
  sheet:  0.24 (0.32), residues: 272
  loop : -3.47 (0.24), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 216 
 HIS   0.001   0.000   HIS G 185 
 PHE   0.006   0.001   PHE G 165 
 TYR   0.005   0.000   TYR C 110 
 ARG   0.002   0.000   ARG G 132 

*********************** 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  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8526 (m-80) cc_final: 0.7894 (m-80)
REVERT: E  171 PHE cc_start: 0.7941 (t80) cc_final: 0.7092 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1732
  time to fit residues: 8.3211
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0030
   chunk 14 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.8006
-------------------------------------------------------------------------------
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 = 0.4529 r_free = 0.4529 target = 0.183614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.132610 restraints weight = 1229.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.137720 restraints weight = 885.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.142076 restraints weight = 683.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5430
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7600  Z= 0.201
  Angle     :  0.582   5.102  10200  Z= 0.314
  Chirality :  0.043   0.138   1080
  Planarity :  0.003   0.014   1248
  Dihedral  :  4.079  12.282    984
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.26), residues: 880
  helix:  0.22 (0.29), residues: 280
  sheet: -0.12 (0.32), residues: 272
  loop : -3.07 (0.25), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP I 216 
 HIS   0.002   0.001   HIS C 185 
 PHE   0.006   0.002   PHE J 189 
 TYR   0.004   0.001   TYR C 176 
 ARG   0.004   0.001   ARG G 132 

*********************** 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  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8569 (m-80) cc_final: 0.7889 (m-80)
REVERT: E  162 CYS cc_start: 0.9172 (p) cc_final: 0.8965 (p)
REVERT: E  171 PHE cc_start: 0.7987 (t80) cc_final: 0.7260 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1933
  time to fit residues: 9.0112
Evaluate side-chains
  34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    0.3980
   chunk 78 optimal weight:    0.0060
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0170
   chunk 79 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0470
   overall best weight:    0.2532
-------------------------------------------------------------------------------
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 = 0.4642 r_free = 0.4642 target = 0.193339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.142233 restraints weight = 1292.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.147134 restraints weight = 961.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.150831 restraints weight = 766.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5402
moved from start:          0.5400

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= 0.135
  Angle     :  0.607   5.448  10200  Z= 0.330
  Chirality :  0.045   0.138   1080
  Planarity :  0.003   0.014   1248
  Dihedral  :  4.242  16.753    984
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  2.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.25), residues: 880
  helix:  0.11 (0.29), residues: 280
  sheet: -0.55 (0.29), residues: 272
  loop : -3.16 (0.25), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP D 216 
 HIS   0.001   0.001   HIS F 185 
 PHE   0.003   0.001   PHE D 194 
 TYR   0.005   0.001   TYR E 176 
 ARG   0.003   0.001   ARG D 119 

*********************** 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
  43 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8536 (m-80) cc_final: 0.7891 (m-80)
REVERT: E  126 ILE cc_start: 0.7480 (pt) cc_final: 0.7229 (pt)
REVERT: E  162 CYS cc_start: 0.9295 (p) cc_final: 0.9084 (p)
REVERT: E  171 PHE cc_start: 0.8007 (t80) cc_final: 0.7190 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.1630
  time to fit residues: 7.3621
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  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    0.0370
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 71 optimal weight:    0.2980
   chunk 74 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5058
-------------------------------------------------------------------------------
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 = 0.4590 r_free = 0.4590 target = 0.191297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.138412 restraints weight = 1231.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.143840 restraints weight = 902.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.148307 restraints weight = 708.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5474
moved from start:          0.5736

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= 0.140
  Angle     :  0.720  10.745  10200  Z= 0.375
  Chirality :  0.046   0.134   1080
  Planarity :  0.002   0.012   1248
  Dihedral  :  4.339  15.227    984
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.31
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.26), residues: 880
  helix:  0.28 (0.29), residues: 280
  sheet: -0.52 (0.32), residues: 272
  loop : -3.12 (0.25), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP E 196 
 HIS   0.001   0.000   HIS J 185 
 PHE   0.014   0.001   PHE C 165 
 TYR   0.006   0.001   TYR E 176 
 ARG   0.003   0.000   ARG F 119 

*********************** 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
  40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8524 (m-80) cc_final: 0.7868 (m-80)
REVERT: E  173 LYS cc_start: 0.8338 (tmtt) cc_final: 0.7992 (mmtm)
REVERT: E  174 THR cc_start: 0.8005 (p) cc_final: 0.7374 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1940
  time to fit residues: 8.3816
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  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0870
   chunk 78 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 63 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.4358
-------------------------------------------------------------------------------
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 = 0.4606 r_free = 0.4606 target = 0.195990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.137420 restraints weight = 1172.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.143098 restraints weight = 854.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.147863 restraints weight = 672.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5390
moved from start:          0.6222

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= 0.146
  Angle     :  0.655   8.683  10200  Z= 0.343
  Chirality :  0.045   0.133   1080
  Planarity :  0.002   0.012   1248
  Dihedral  :  4.156  13.507    984
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.84
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.26), residues: 880
  helix:  0.22 (0.29), residues: 288
  sheet: -0.65 (0.32), residues: 272
  loop : -3.22 (0.24), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP E 196 
 HIS   0.001   0.001   HIS I 185 
 PHE   0.011   0.002   PHE C 165 
 TYR   0.009   0.001   TYR G 123 
 ARG   0.003   0.000   ARG C 119 

*********************** 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
  39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8555 (m-80) cc_final: 0.7883 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1734
  time to fit residues: 7.3352
Evaluate side-chains
  34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0010
   chunk 78 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.7788
-------------------------------------------------------------------------------
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 = 0.4593 r_free = 0.4593 target = 0.195314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.136262 restraints weight = 1220.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.141837 restraints weight = 906.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.145508 restraints weight = 720.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5456
moved from start:          0.6346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7600  Z= 0.151
  Angle     :  0.616   6.718  10200  Z= 0.336
  Chirality :  0.044   0.131   1080
  Planarity :  0.002   0.012   1248
  Dihedral  :  4.268  13.533    984
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.26), residues: 880
  helix:  0.21 (0.29), residues: 288
  sheet: -0.60 (0.32), residues: 272
  loop : -3.08 (0.25), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP G 196 
 HIS   0.001   0.001   HIS I 185 
 PHE   0.012   0.001   PHE C 165 
 TYR   0.005   0.001   TYR J 164 
 ARG   0.002   0.000   ARG F 119 

*********************** 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  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8585 (m-80) cc_final: 0.7892 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1526
  time to fit residues: 6.9001
Evaluate side-chains
  36 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   overall best weight:    0.8180
-------------------------------------------------------------------------------
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 = 0.4619 r_free = 0.4619 target = 0.194194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.137349 restraints weight = 1249.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.143272 restraints weight = 914.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.148166 restraints weight = 720.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5480
moved from start:          0.6564

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= 0.162
  Angle     :  0.627   5.739  10200  Z= 0.348
  Chirality :  0.045   0.134   1080
  Planarity :  0.003   0.012   1248
  Dihedral  :  4.524  18.158    984
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 11.50
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.24), residues: 880
  helix:  0.20 (0.29), residues: 280
  sheet:  0.96 (0.37), residues: 168
  loop : -3.42 (0.19), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP E 196 
 HIS   0.001   0.001   HIS C 185 
 PHE   0.010   0.002   PHE F 171 
 TYR   0.011   0.001   TYR I 123 
 ARG   0.002   0.000   ARG C 119 

*********************** 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
  40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8603 (m-80) cc_final: 0.7914 (m-80)
REVERT: E  124 LYS cc_start: 0.8063 (tptt) cc_final: 0.7793 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1654
  time to fit residues: 7.1045
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0270
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.5838
-------------------------------------------------------------------------------
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 = 0.4633 r_free = 0.4633 target = 0.192573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.136431 restraints weight = 1181.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.141881 restraints weight = 857.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.146670 restraints weight = 673.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5460
moved from start:          0.6780

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= 0.155
  Angle     :  0.675   5.960  10200  Z= 0.379
  Chirality :  0.046   0.137   1080
  Planarity :  0.003   0.012   1248
  Dihedral  :  4.490  18.016    984
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.10
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.25), residues: 880
  helix:  0.05 (0.29), residues: 288
  sheet:  1.23 (0.40), residues: 168
  loop : -3.45 (0.20), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP F 196 
 HIS   0.002   0.001   HIS C 185 
 PHE   0.012   0.002   PHE H 165 
 TYR   0.006   0.001   TYR F 123 
 ARG   0.002   0.000   ARG D 119 

********************** 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
  41 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  113 TYR cc_start: 0.8606 (m-80) cc_final: 0.7920 (m-80)
REVERT: E  124 LYS cc_start: 0.7922 (tptt) cc_final: 0.7673 (tppt)
REVERT: E  173 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7675 (mmtt)
REVERT: E  174 THR cc_start: 0.7964 (p) cc_final: 0.7206 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1702
  time to fit residues: 7.5322
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  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    0.0670
   chunk 33 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.3722
-------------------------------------------------------------------------------
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 = 0.188502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.130247 restraints weight = 1306.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.136107 restraints weight = 944.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.140228 restraints weight = 735.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
moved from start:          0.6879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7600  Z= 0.175
  Angle     :  0.629   5.094  10200  Z= 0.352
  Chirality :  0.045   0.141   1080
  Planarity :  0.003   0.012   1248
  Dihedral  :  4.859  24.626    984
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.90
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.25), residues: 880
  helix:  0.08 (0.28), residues: 288
  sheet: -0.02 (0.38), residues: 184
  loop : -3.32 (0.21), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP E 196 
 HIS   0.002   0.002   HIS H 185 
 PHE   0.017   0.002   PHE G 165 
 TYR   0.008   0.001   TYR F 123 
 ARG   0.002   0.001   ARG D 119 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1844.45 seconds
wall clock time: 32 minutes 59.73 seconds (1979.73 seconds total)