Starting phenix.real_space_refine
on Tue Mar  3 18:59:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2026/7agg_11779.map"
  }
  resolution = 3.3
  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=   0.001
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      33      5.16       5
     C    5206      2.51       5
     N    1344      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 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: 8252
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1538
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 190}
    Chain: "D"
      Number of atoms: 1819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1819
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
    Chain: "B"
      Number of atoms: 1538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1538
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 1538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1538
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 1819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1819
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
  Time building chain proxies: 1.76, per 1000 atoms: 0.21
  Number of scatterers: 8252
  At special positions: 0
  Unit cell: (113.75, 110.5, 101.4, 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      33     16.00
     O    1669      8.00
     N    1344      7.00
     C    5206      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: 0.51
  Conformation dependent library (CDL) restraints added in 301.7 milliseconds
  

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 17 sheets defined
      7.5% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.558A  pdb=" N   GLY A 234 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 252
      removed outlier: 5.642A  pdb=" N   LYS A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU A 252 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 296
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.558A  pdb=" N   GLY B 234 " --> pdb=" O   ASN B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 252
      removed outlier: 5.642A  pdb=" N   LYS B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU B 252 " --> pdb=" O   ARG B 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 184
    Processing helix  chain 'C' and resid 185 through 188
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.557A  pdb=" N   GLY C 234 " --> pdb=" O   ASN C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 252
      removed outlier: 5.642A  pdb=" N   LYS C 251 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU C 252 " --> pdb=" O   ARG C 249 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 292 through 296
    Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135
      removed outlier: 3.573A  pdb=" N   TYR A 320 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199
      removed outlier: 5.896A  pdb=" N   ASN A 297 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 120
      removed outlier: 6.990A  pdb=" N   THR D 187 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU D 154 " --> pdb=" O   THR D 187 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR D 189 " --> pdb=" O   VAL D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 131
      removed outlier: 3.579A  pdb=" N   MET D 130 " --> pdb=" O   ILE D 171 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 222 through 223
    Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 231
      removed outlier: 6.723A  pdb=" N   SER D 302 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 135
      removed outlier: 3.573A  pdb=" N   TYR B 320 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 190 through 199
      removed outlier: 5.896A  pdb=" N   ASN B 297 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220
    Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135
      removed outlier: 3.572A  pdb=" N   TYR C 320 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 190 through 199
      removed outlier: 5.897A  pdb=" N   ASN C 297 " --> pdb=" O   PRO C 270 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 219 through 220
    Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 120
      removed outlier: 6.991A  pdb=" N   THR F 187 " --> pdb=" O   LEU F 154 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU F 154 " --> pdb=" O   THR F 187 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   THR F 189 " --> pdb=" O   VAL F 152 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 131
      removed outlier: 3.578A  pdb=" N   MET F 130 " --> pdb=" O   ILE F 171 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 222 through 223
    Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 231
      removed outlier: 6.725A  pdb=" N   SER F 302 " --> pdb=" O   ALA F 264 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    537 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: 1.05

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2700
        1.34 -     1.46: 1662
        1.46 -     1.57: 4002
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 8418
  Sorted by residual:
  bond pdb=" CB  TRP C 135 "
       pdb=" CG  TRP C 135 "
    ideal  model  delta    sigma   weight residual
    1.498  1.443  0.055 3.10e-02 1.04e+03 3.10e+00
  bond pdb=" CB  TRP A 135 "
       pdb=" CG  TRP A 135 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.06e+00
  bond pdb=" CB  TRP B 135 "
       pdb=" CG  TRP B 135 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.03e+00
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.457  0.056 3.90e-02 6.57e+02 2.09e+00
  bond pdb=" CG1 ILE A 273 "
       pdb=" CD1 ILE A 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.457  0.056 3.90e-02 6.57e+02 2.08e+00
  ... (remaining 8413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 10498
        1.26 -     2.52: 791
        2.52 -     3.77: 144
        3.77 -     5.03: 48
        5.03 -     6.29: 9
  Bond angle restraints: 11490
  Sorted by residual:
  angle pdb=" N   TRP A 135 "
        pdb=" CA  TRP A 135 "
        pdb=" CB  TRP A 135 "
      ideal   model   delta    sigma   weight residual
     111.56  106.66    4.90 1.52e+00 4.33e-01 1.04e+01
  angle pdb=" N   TRP C 135 "
        pdb=" CA  TRP C 135 "
        pdb=" CB  TRP C 135 "
      ideal   model   delta    sigma   weight residual
     111.56  106.66    4.90 1.52e+00 4.33e-01 1.04e+01
  angle pdb=" N   TRP B 135 "
        pdb=" CA  TRP B 135 "
        pdb=" CB  TRP B 135 "
      ideal   model   delta    sigma   weight residual
     111.56  106.68    4.88 1.52e+00 4.33e-01 1.03e+01
  angle pdb=" C   LYS D 313 "
        pdb=" CA  LYS D 313 "
        pdb=" CB  LYS D 313 "
      ideal   model   delta    sigma   weight residual
     110.96  106.03    4.93 1.54e+00 4.22e-01 1.03e+01
  angle pdb=" C   LYS F 313 "
        pdb=" CA  LYS F 313 "
        pdb=" CB  LYS F 313 "
      ideal   model   delta    sigma   weight residual
     110.96  106.03    4.93 1.54e+00 4.22e-01 1.02e+01
  ... (remaining 11485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 4637
       17.28 -    34.56: 311
       34.56 -    51.85: 44
       51.85 -    69.13: 19
       69.13 -    86.41: 8
  Dihedral angle restraints: 5019
    sinusoidal: 1907
      harmonic: 3112
  Sorted by residual:
  dihedral pdb=" CA  GLU D 240 "
           pdb=" C   GLU D 240 "
           pdb=" N   VAL D 241 "
           pdb=" CA  VAL D 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  GLU F 240 "
           pdb=" C   GLU F 240 "
           pdb=" N   VAL F 241 "
           pdb=" CA  VAL F 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.72  -25.28     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ILE F 315 "
           pdb=" C   ILE F 315 "
           pdb=" N   ARG F 316 "
           pdb=" CA  ARG F 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.57   24.43     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1024
       0.057 -    0.115: 292
       0.115 -    0.172: 39
       0.172 -    0.230: 0
       0.230 -    0.287: 2
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CB  VAL D 204 "
            pdb=" CA  VAL D 204 "
            pdb=" CG1 VAL D 204 "
            pdb=" CG2 VAL D 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  VAL F 204 "
            pdb=" CA  VAL F 204 "
            pdb=" CG1 VAL F 204 "
            pdb=" CG2 VAL F 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  TYR F 158 "
            pdb=" N   TYR F 158 "
            pdb=" C   TYR F 158 "
            pdb=" CB  TYR F 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 135 "   -0.040 2.00e-02 2.50e+03   4.40e-02 4.83e+01
        pdb=" CG  TRP A 135 "    0.113 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 135 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 135 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 135 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 135 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 135 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 135 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 135 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 135 "   -0.040 2.00e-02 2.50e+03   4.39e-02 4.82e+01
        pdb=" CG  TRP C 135 "    0.113 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 135 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 135 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 135 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 135 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 135 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 135 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 135 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 135 "    0.040 2.00e-02 2.50e+03   4.39e-02 4.81e+01
        pdb=" CG  TRP B 135 "   -0.113 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 135 "    0.067 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 135 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 135 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 135 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 135 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 135 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 135 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 74
        2.56 -     3.15: 6661
        3.15 -     3.73: 12795
        3.73 -     4.32: 18999
        4.32 -     4.90: 30816
  Nonbonded interactions: 69345
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 319 "
            pdb=" OH  TYR B 319 "
     model   vdw
     1.980 3.040
  nonbonded pdb=" O   HIS F 273 "
            pdb=" OG1 THR F 286 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   HIS D 273 "
            pdb=" OG1 THR D 286 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER A 238 "
            pdb=" OE1 GLN B 222 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG1 THR B 165 "
            pdb=" OG1 THR B 170 "
     model   vdw
     2.292 3.040
  ... (remaining 69340 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 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.810
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.050
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
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      :  0.007   0.056   8418  Z= 0.323
  Angle     :  0.785   6.289  11490  Z= 0.455
  Chirality :  0.052   0.287   1357
  Planarity :  0.005   0.050   1484
  Dihedral  : 13.158  86.411   3001
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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: -1.18 (0.26), residues: 1046
  helix: -2.40 (0.61), residues: 54
  sheet: -0.53 (0.26), residues: 370
  loop : -0.73 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG C 280 
 TYR   0.038   0.003   TYR F 293 
 PHE   0.016   0.002   PHE B 199 
 TRP   0.113   0.010   TRP A 135 
 HIS   0.007   0.002   HIS F 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00716 ( 8418)
  covalent geometry    : angle       0.78525 (11490)
  hydrogen bonds       : bond        0.23069 (  220)
  hydrogen bonds       : angle      10.49570 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 THR cc_start: 0.8912 (p) cc_final: 0.8560 (t)
REVERT: B  156 CYS cc_start: 0.6660 (p) cc_final: 0.6230 (p)
REVERT: F  189 THR cc_start: 0.7935 (m) cc_final: 0.7226 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0960
  time to fit residues: 28.9989
Evaluate side-chains
  146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
D 112 GLN
D 206 GLN
D 208 GLN
B 188 HIS
** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.118235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.091518 restraints weight = 17689.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 3.88
r_work: 0.3319 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8418  Z= 0.130
  Angle     :  0.564   5.574  11490  Z= 0.306
  Chirality :  0.046   0.162   1357
  Planarity :  0.004   0.049   1484
  Dihedral  :  5.544  23.486   1121
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.27 %
    Favored  : 89.99 %
  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: -0.88 (0.26), residues: 1046
  helix: -1.86 (0.79), residues: 36
  sheet: -0.38 (0.27), residues: 376
  loop : -0.57 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 212 
 TYR   0.021   0.001   TYR D 293 
 PHE   0.016   0.002   PHE D 301 
 TRP   0.034   0.004   TRP A 135 
 HIS   0.002   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8418)
  covalent geometry    : angle       0.56436 (11490)
  hydrogen bonds       : bond        0.03261 (  220)
  hydrogen bonds       : angle       7.31396 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 167
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7263 (mm-30)
REVERT: A  323 GLU cc_start: 0.8616 (tp30) cc_final: 0.8343 (tp30)
REVERT: A  325 ASP cc_start: 0.8081 (m-30) cc_final: 0.7816 (m-30)
REVERT: D  154 LEU cc_start: 0.8847 (mp) cc_final: 0.8595 (mp)
REVERT: D  167 ASP cc_start: 0.8374 (p0) cc_final: 0.8120 (p0)
REVERT: D  174 THR cc_start: 0.9001 (p) cc_final: 0.8695 (t)
REVERT: B  184 MET cc_start: 0.8339 (ppp) cc_final: 0.8100 (ppp)
REVERT: B  276 MET cc_start: 0.8029 (mtm) cc_final: 0.7543 (ttt)
REVERT: C  200 ASP cc_start: 0.7872 (t0) cc_final: 0.7624 (t0)
REVERT: C  250 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8213 (mt-10)
REVERT: F  150 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6385 (ptt180)
REVERT: F  189 THR cc_start: 0.7573 (m) cc_final: 0.6934 (p)
REVERT: F  191 GLU cc_start: 0.7908 (tt0) cc_final: 0.7247 (tt0)
REVERT: F  206 GLN cc_start: 0.7575 (mt0) cc_final: 0.7328 (mp10)
REVERT: F  300 ASP cc_start: 0.8773 (t0) cc_final: 0.7957 (p0)
REVERT: F  301 PHE cc_start: 0.8456 (p90) cc_final: 0.7919 (p90)
  outliers start: 7
  outliers final: 6
  residues processed: 172
  average time/residue: 0.0917
  time to fit residues: 21.5459
Evaluate side-chains
  150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  177 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0270
   overall best weight:    2.0046

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

Flipped N/Q/H residues before XYZ refinement:
D 112 GLN
D 208 GLN
B 146 GLN
B 305 GLN
C 231 ASN
F 106 ASN
** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.112445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.085799 restraints weight = 18059.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.80
r_work: 0.3219 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8418  Z= 0.183
  Angle     :  0.564   6.039  11490  Z= 0.304
  Chirality :  0.045   0.147   1357
  Planarity :  0.004   0.041   1484
  Dihedral  :  5.325  23.795   1121
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.71 %
    Favored  : 86.58 %
  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: -0.84 (0.26), residues: 1046
  helix: -1.01 (1.12), residues: 21
  sheet: -0.32 (0.27), residues: 370
  loop : -0.64 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 291 
 TYR   0.018   0.001   TYR D 293 
 PHE   0.017   0.002   PHE C 198 
 TRP   0.032   0.003   TRP C 135 
 HIS   0.004   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8418)
  covalent geometry    : angle       0.56354 (11490)
  hydrogen bonds       : bond        0.03133 (  220)
  hydrogen bonds       : angle       6.76878 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9136 (tt0) cc_final: 0.8591 (tt0)
REVERT: A  196 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7306 (mm-30)
REVERT: A  276 MET cc_start: 0.7845 (mtp) cc_final: 0.7305 (ttp)
REVERT: A  279 GLN cc_start: 0.7780 (pm20) cc_final: 0.6646 (pm20)
REVERT: A  323 GLU cc_start: 0.8759 (tp30) cc_final: 0.8459 (tp30)
REVERT: A  325 ASP cc_start: 0.8366 (m-30) cc_final: 0.8158 (m-30)
REVERT: D  154 LEU cc_start: 0.8795 (mp) cc_final: 0.8580 (mp)
REVERT: D  167 ASP cc_start: 0.8324 (p0) cc_final: 0.8040 (p0)
REVERT: B  129 ASP cc_start: 0.8346 (t0) cc_final: 0.7883 (t0)
REVERT: B  192 ASN cc_start: 0.9095 (t0) cc_final: 0.8398 (p0)
REVERT: B  276 MET cc_start: 0.8105 (mtm) cc_final: 0.7586 (ttt)
REVERT: B  323 GLU cc_start: 0.8191 (tp30) cc_final: 0.7717 (tp30)
REVERT: B  325 ASP cc_start: 0.7788 (m-30) cc_final: 0.7524 (m-30)
REVERT: C  250 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8174 (mt-10)
REVERT: F  150 ARG cc_start: 0.7440 (ptt180) cc_final: 0.6622 (ptt180)
REVERT: F  189 THR cc_start: 0.7709 (m) cc_final: 0.6986 (p)
REVERT: F  191 GLU cc_start: 0.7939 (tt0) cc_final: 0.7396 (tt0)
REVERT: F  206 GLN cc_start: 0.7635 (mt0) cc_final: 0.7352 (mp10)
REVERT: F  301 PHE cc_start: 0.8433 (p90) cc_final: 0.8093 (p90)
  outliers start: 16
  outliers final: 11
  residues processed: 163
  average time/residue: 0.0916
  time to fit residues: 20.6686
Evaluate side-chains
  148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  252 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  106 ASN
Chi-restraints excluded: chain F residue  177 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0870
   chunk 76 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9980
   chunk 63 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0570
   chunk 16 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
D 206 GLN
D 208 GLN
C 279 GLN
F 106 ASN
** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.117676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.091076 restraints weight = 18407.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.90
r_work: 0.3342 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8418  Z= 0.092
  Angle     :  0.488   4.961  11490  Z= 0.264
  Chirality :  0.044   0.149   1357
  Planarity :  0.003   0.041   1484
  Dihedral  :  4.768  20.599   1121
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.71 %
    Favored  : 86.58 %
  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: -0.71 (0.26), residues: 1046
  helix: -0.90 (1.11), residues: 21
  sheet: -0.22 (0.27), residues: 370
  loop : -0.56 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 212 
 TYR   0.021   0.001   TYR D 293 
 PHE   0.014   0.002   PHE F 110 
 TRP   0.015   0.002   TRP A 296 
 HIS   0.001   0.000   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8418)
  covalent geometry    : angle       0.48828 (11490)
  hydrogen bonds       : bond        0.02420 (  220)
  hydrogen bonds       : angle       6.35702 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.9060 (tt0) cc_final: 0.8768 (tt0)
REVERT: A  184 MET cc_start: 0.8592 (tpp) cc_final: 0.8327 (tpp)
REVERT: A  196 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: D  120 GLU cc_start: 0.8545 (tt0) cc_final: 0.8263 (tt0)
REVERT: D  167 ASP cc_start: 0.8254 (p0) cc_final: 0.7931 (p0)
REVERT: D  206 GLN cc_start: 0.8069 (tt0) cc_final: 0.7839 (pm20)
REVERT: B  129 ASP cc_start: 0.8256 (t0) cc_final: 0.7773 (t0)
REVERT: B  192 ASN cc_start: 0.8927 (t0) cc_final: 0.8550 (p0)
REVERT: B  251 LYS cc_start: 0.9208 (mttm) cc_final: 0.8944 (mttt)
REVERT: B  276 MET cc_start: 0.7914 (mtm) cc_final: 0.7538 (ttt)
REVERT: B  279 GLN cc_start: 0.7064 (pm20) cc_final: 0.6844 (pm20)
REVERT: B  323 GLU cc_start: 0.8059 (tp30) cc_final: 0.7787 (tp30)
REVERT: C  189 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8633 (mtmm)
REVERT: C  200 ASP cc_start: 0.7750 (t0) cc_final: 0.7531 (t0)
REVERT: C  250 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8194 (mt-10)
REVERT: F  110 PHE cc_start: 0.6527 (m-10) cc_final: 0.6045 (m-10)
REVERT: F  150 ARG cc_start: 0.7354 (ptt180) cc_final: 0.6499 (ptt180)
REVERT: F  172 TYR cc_start: 0.8396 (m-80) cc_final: 0.8163 (m-80)
REVERT: F  189 THR cc_start: 0.7529 (m) cc_final: 0.6914 (p)
REVERT: F  191 GLU cc_start: 0.8001 (tt0) cc_final: 0.7361 (tt0)
REVERT: F  206 GLN cc_start: 0.7882 (mt0) cc_final: 0.7461 (mp10)
REVERT: F  327 LYS cc_start: 0.7900 (ptpp) cc_final: 0.7498 (pttm)
  outliers start: 16
  outliers final: 8
  residues processed: 176
  average time/residue: 0.0994
  time to fit residues: 23.3069
Evaluate side-chains
  154 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  300 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 64 optimal weight:    0.0970
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   overall best weight:    3.7784

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

Flipped N/Q/H residues before XYZ refinement:
D 217 ASN
B 305 GLN
C 188 HIS
F 106 ASN
F 219 ASN
F 236 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.107979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.081305 restraints weight = 18855.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 4.00
r_work: 0.3130 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8418  Z= 0.300
  Angle     :  0.646   6.555  11490  Z= 0.345
  Chirality :  0.047   0.143   1357
  Planarity :  0.004   0.043   1484
  Dihedral  :  5.518  23.902   1121
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.46 %
    Favored  : 84.77 %
  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: -1.17 (0.26), residues: 1046
  helix: -2.17 (0.76), residues: 36
  sheet: -0.68 (0.26), residues: 382
  loop : -0.68 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 291 
 TYR   0.021   0.002   TYR F 293 
 PHE   0.022   0.002   PHE A 199 
 TRP   0.027   0.004   TRP C 135 
 HIS   0.008   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 ( 8418)
  covalent geometry    : angle       0.64613 (11490)
  hydrogen bonds       : bond        0.03478 (  220)
  hydrogen bonds       : angle       6.71569 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9180 (tt0) cc_final: 0.8716 (tt0)
REVERT: D  120 GLU cc_start: 0.8641 (tt0) cc_final: 0.8439 (tt0)
REVERT: D  167 ASP cc_start: 0.8224 (p0) cc_final: 0.8021 (p0)
REVERT: D  170 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8539 (mt-10)
REVERT: D  217 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.6972 (m-40)
REVERT: B  129 ASP cc_start: 0.8414 (t0) cc_final: 0.8050 (t0)
REVERT: B  276 MET cc_start: 0.8362 (mtm) cc_final: 0.7844 (ttt)
REVERT: B  325 ASP cc_start: 0.7808 (m-30) cc_final: 0.7569 (m-30)
REVERT: C  250 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: F  150 ARG cc_start: 0.7761 (ptt180) cc_final: 0.7115 (ptt180)
REVERT: F  167 ASP cc_start: 0.8347 (p0) cc_final: 0.8011 (p0)
REVERT: F  189 THR cc_start: 0.7684 (m) cc_final: 0.7035 (p)
REVERT: F  191 GLU cc_start: 0.8058 (tt0) cc_final: 0.7827 (tt0)
REVERT: F  206 GLN cc_start: 0.7805 (mt0) cc_final: 0.7259 (mp10)
REVERT: F  293 TYR cc_start: 0.4177 (p90) cc_final: 0.3678 (p90)
REVERT: F  327 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7753 (ptpp)
  outliers start: 26
  outliers final: 20
  residues processed: 164
  average time/residue: 0.0930
  time to fit residues: 20.7824
Evaluate side-chains
  156 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  309 THR
Chi-restraints excluded: chain F residue  106 ASN
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  300 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 ASN
** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.109618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.083009 restraints weight = 18686.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 3.98
r_work: 0.3167 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8418  Z= 0.178
  Angle     :  0.570   7.980  11490  Z= 0.303
  Chirality :  0.045   0.150   1357
  Planarity :  0.004   0.041   1484
  Dihedral  :  5.140  20.833   1121
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.70 %
    Favored  : 83.17 %
  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: -1.13 (0.26), residues: 1046
  helix: -1.92 (0.82), residues: 36
  sheet: -0.68 (0.26), residues: 382
  loop : -0.65 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 291 
 TYR   0.018   0.001   TYR D 293 
 PHE   0.016   0.002   PHE F 110 
 TRP   0.016   0.003   TRP C 296 
 HIS   0.004   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8418)
  covalent geometry    : angle       0.57046 (11490)
  hydrogen bonds       : bond        0.02829 (  220)
  hydrogen bonds       : angle       6.45182 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9155 (tt0) cc_final: 0.8698 (tt0)
REVERT: D  167 ASP cc_start: 0.8229 (p0) cc_final: 0.8011 (p0)
REVERT: D  170 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: D  217 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6940 (m-40)
REVERT: D  243 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8056 (mtp85)
REVERT: B  129 ASP cc_start: 0.8456 (t0) cc_final: 0.8097 (t0)
REVERT: B  276 MET cc_start: 0.8182 (mtm) cc_final: 0.7914 (ttt)
REVERT: B  323 GLU cc_start: 0.8256 (tp30) cc_final: 0.7806 (tp30)
REVERT: B  325 ASP cc_start: 0.7744 (m-30) cc_final: 0.7502 (m-30)
REVERT: C  189 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8517 (mtmm)
REVERT: C  250 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: F  150 ARG cc_start: 0.7762 (ptt180) cc_final: 0.7094 (ptt180)
REVERT: F  167 ASP cc_start: 0.8356 (p0) cc_final: 0.8022 (p0)
REVERT: F  189 THR cc_start: 0.7621 (m) cc_final: 0.7007 (p)
REVERT: F  191 GLU cc_start: 0.8222 (tt0) cc_final: 0.7672 (tt0)
REVERT: F  293 TYR cc_start: 0.3977 (p90) cc_final: 0.3512 (p90)
REVERT: F  301 PHE cc_start: 0.8392 (p90) cc_final: 0.8090 (p90)
  outliers start: 20
  outliers final: 14
  residues processed: 158
  average time/residue: 0.0995
  time to fit residues: 21.4251
Evaluate side-chains
  155 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  243 ARG
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  300 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0030
   chunk 85 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 84 optimal weight:   20.0000
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
D 217 ASN
F 106 ASN
F 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.111244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.085600 restraints weight = 18744.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 3.83
r_work: 0.3199 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8418  Z= 0.137
  Angle     :  0.550   7.135  11490  Z= 0.290
  Chirality :  0.044   0.151   1357
  Planarity :  0.003   0.040   1484
  Dihedral  :  4.874  17.946   1121
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.59 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.26), residues: 1046
  helix: -1.84 (0.84), residues: 36
  sheet: -0.60 (0.26), residues: 382
  loop : -0.59 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 291 
 TYR   0.017   0.001   TYR D 293 
 PHE   0.015   0.002   PHE A 172 
 TRP   0.014   0.002   TRP C 296 
 HIS   0.002   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8418)
  covalent geometry    : angle       0.55012 (11490)
  hydrogen bonds       : bond        0.02614 (  220)
  hydrogen bonds       : angle       6.27646 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9108 (tt0) cc_final: 0.8660 (tt0)
REVERT: D  112 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7309 (tm-30)
REVERT: D  150 ARG cc_start: 0.9036 (ptt-90) cc_final: 0.8804 (ptt-90)
REVERT: D  167 ASP cc_start: 0.8226 (p0) cc_final: 0.7980 (p0)
REVERT: D  206 GLN cc_start: 0.7952 (tt0) cc_final: 0.7358 (tm-30)
REVERT: D  217 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.6626 (m-40)
REVERT: D  240 GLU cc_start: 0.8284 (pm20) cc_final: 0.8075 (pm20)
REVERT: D  243 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8025 (mtp85)
REVERT: B  129 ASP cc_start: 0.8441 (t0) cc_final: 0.8035 (t0)
REVERT: B  251 LYS cc_start: 0.9156 (mttm) cc_final: 0.8892 (mttm)
REVERT: B  276 MET cc_start: 0.8262 (mtm) cc_final: 0.8047 (mpp)
REVERT: B  323 GLU cc_start: 0.8194 (tp30) cc_final: 0.7808 (tp30)
REVERT: C  184 MET cc_start: 0.8655 (tmm) cc_final: 0.8302 (tmm)
REVERT: C  250 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: F  150 ARG cc_start: 0.7796 (ptt180) cc_final: 0.7016 (ptt180)
REVERT: F  167 ASP cc_start: 0.8362 (p0) cc_final: 0.8009 (p0)
REVERT: F  191 GLU cc_start: 0.7971 (tt0) cc_final: 0.7355 (tt0)
REVERT: F  301 PHE cc_start: 0.8308 (p90) cc_final: 0.8014 (p90)
  outliers start: 25
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0982
  time to fit residues: 22.2434
Evaluate side-chains
  162 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  243 ARG
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  156 CYS
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  106 ASN
Chi-restraints excluded: chain F residue  177 THR
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  300 ASP
Chi-restraints excluded: chain F residue  305 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
D 217 ASN
F 106 ASN
F 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.104379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.079540 restraints weight = 18729.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 3.72
r_work: 0.3109 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.065   8418  Z= 0.376
  Angle     :  0.733   7.606  11490  Z= 0.390
  Chirality :  0.049   0.175   1357
  Planarity :  0.004   0.049   1484
  Dihedral  :  5.814  24.786   1121
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.38 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.26), residues: 1046
  helix: -2.12 (0.76), residues: 36
  sheet: -0.88 (0.26), residues: 382
  loop : -0.88 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 193 
 TYR   0.022   0.002   TYR F 293 
 PHE   0.025   0.003   PHE A 199 
 TRP   0.024   0.004   TRP A 296 
 HIS   0.010   0.002   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00852 ( 8418)
  covalent geometry    : angle       0.73292 (11490)
  hydrogen bonds       : bond        0.03699 (  220)
  hydrogen bonds       : angle       6.76110 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  324 ASP cc_start: 0.7735 (m-30) cc_final: 0.7465 (t0)
REVERT: D  150 ARG cc_start: 0.8972 (ptt-90) cc_final: 0.8754 (ptt180)
REVERT: D  243 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8143 (mtp85)
REVERT: B  129 ASP cc_start: 0.8476 (t0) cc_final: 0.8101 (t0)
REVERT: B  276 MET cc_start: 0.8487 (mtm) cc_final: 0.8096 (ttt)
REVERT: C  250 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: F  167 ASP cc_start: 0.8530 (p0) cc_final: 0.8158 (p0)
REVERT: F  301 PHE cc_start: 0.8356 (p90) cc_final: 0.8058 (p90)
  outliers start: 32
  outliers final: 26
  residues processed: 165
  average time/residue: 0.0953
  time to fit residues: 21.5707
Evaluate side-chains
  157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  243 ARG
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  274 SER
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  309 THR
Chi-restraints excluded: chain F residue  106 ASN
Chi-restraints excluded: chain F residue  177 THR
Chi-restraints excluded: chain F residue  215 ASP
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  282 GLU
Chi-restraints excluded: chain F residue  305 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
D 217 ASN
F 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.109942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.084339 restraints weight = 18802.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 3.87
r_work: 0.3194 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8418  Z= 0.130
  Angle     :  0.578   8.607  11490  Z= 0.307
  Chirality :  0.045   0.159   1357
  Planarity :  0.004   0.043   1484
  Dihedral  :  5.113  30.425   1121
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.34 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.14 (0.27), residues: 1046
  helix: -1.93 (0.71), residues: 54
  sheet: -0.64 (0.26), residues: 378
  loop : -0.64 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 193 
 TYR   0.024   0.002   TYR D 293 
 PHE   0.015   0.002   PHE A 172 
 TRP   0.011   0.002   TRP B 296 
 HIS   0.002   0.000   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8418)
  covalent geometry    : angle       0.57770 (11490)
  hydrogen bonds       : bond        0.02693 (  220)
  hydrogen bonds       : angle       6.35707 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9123 (tt0) cc_final: 0.8677 (tt0)
REVERT: A  324 ASP cc_start: 0.7747 (m-30) cc_final: 0.7457 (t0)
REVERT: D  188 LEU cc_start: 0.7976 (mm) cc_final: 0.7697 (tp)
REVERT: D  206 GLN cc_start: 0.7988 (tt0) cc_final: 0.7339 (tm-30)
REVERT: D  217 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6945 (m-40)
REVERT: D  243 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8008 (mtp85)
REVERT: B  129 ASP cc_start: 0.8415 (t0) cc_final: 0.8086 (t0)
REVERT: B  251 LYS cc_start: 0.9144 (mttm) cc_final: 0.8861 (mttt)
REVERT: B  323 GLU cc_start: 0.8309 (tp30) cc_final: 0.7948 (tp30)
REVERT: C  250 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: F  167 ASP cc_start: 0.8529 (p0) cc_final: 0.8175 (p0)
REVERT: F  191 GLU cc_start: 0.7772 (tt0) cc_final: 0.6807 (tp30)
  outliers start: 22
  outliers final: 16
  residues processed: 164
  average time/residue: 0.0894
  time to fit residues: 20.1345
Evaluate side-chains
  158 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  243 ARG
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  305 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 21 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.8182

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

Flipped N/Q/H residues before XYZ refinement:
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 ASN
B 305 GLN
F 106 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.108671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.083846 restraints weight = 18359.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.77
r_work: 0.3184 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8418  Z= 0.169
  Angle     :  0.593   6.838  11490  Z= 0.316
  Chirality :  0.045   0.166   1357
  Planarity :  0.004   0.043   1484
  Dihedral  :  5.121  35.103   1121
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.34 %
    Favored  : 82.43 %
  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: -1.14 (0.26), residues: 1046
  helix: -1.55 (0.90), residues: 36
  sheet: -0.67 (0.26), residues: 380
  loop : -0.70 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 291 
 TYR   0.022   0.002   TYR D 293 
 PHE   0.016   0.002   PHE A 199 
 TRP   0.012   0.002   TRP C 135 
 HIS   0.004   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8418)
  covalent geometry    : angle       0.59250 (11490)
  hydrogen bonds       : bond        0.02826 (  220)
  hydrogen bonds       : angle       6.27926 (  537)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9140 (tt0) cc_final: 0.8688 (tt0)
REVERT: A  324 ASP cc_start: 0.7762 (m-30) cc_final: 0.7465 (t0)
REVERT: D  188 LEU cc_start: 0.7991 (mm) cc_final: 0.7738 (tp)
REVERT: D  217 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6915 (m-40)
REVERT: D  243 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8052 (mtp85)
REVERT: B  129 ASP cc_start: 0.8416 (t0) cc_final: 0.8125 (t0)
REVERT: B  251 LYS cc_start: 0.9137 (mttm) cc_final: 0.8893 (mttt)
REVERT: B  323 GLU cc_start: 0.8354 (tp30) cc_final: 0.7971 (tp30)
REVERT: C  250 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: F  167 ASP cc_start: 0.8503 (p0) cc_final: 0.8146 (p0)
REVERT: F  172 TYR cc_start: 0.8538 (m-80) cc_final: 0.8294 (m-80)
REVERT: F  191 GLU cc_start: 0.7873 (tt0) cc_final: 0.6887 (tp30)
REVERT: F  282 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6070 (pm20)
REVERT: F  300 ASP cc_start: 0.8390 (m-30) cc_final: 0.8046 (p0)
  outliers start: 21
  outliers final: 18
  residues processed: 158
  average time/residue: 0.0911
  time to fit residues: 19.8284
Evaluate side-chains
  156 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain D residue  190 VAL
Chi-restraints excluded: chain D residue  217 ASN
Chi-restraints excluded: chain D residue  243 ARG
Chi-restraints excluded: chain D residue  246 VAL
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  194 THR
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain F residue  106 ASN
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  282 GLU
Chi-restraints excluded: chain F residue  305 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 17 optimal weight:    0.0670
   chunk 30 optimal weight:    0.7980
   chunk 97 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 99 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.8522

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

Flipped N/Q/H residues before XYZ refinement:
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 GLN
F 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.109434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.084032 restraints weight = 18885.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 3.92
r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   8418  Z= 0.204
  Angle     :  0.950  59.195  11490  Z= 0.564
  Chirality :  0.046   0.352   1357
  Planarity :  0.005   0.117   1484
  Dihedral  :  5.184  35.204   1121
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.44 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.10 %
  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: -1.12 (0.26), residues: 1046
  helix: -1.53 (0.90), residues: 36
  sheet: -0.67 (0.26), residues: 380
  loop : -0.68 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 243 
 TYR   0.020   0.002   TYR D 293 
 PHE   0.016   0.002   PHE A 199 
 TRP   0.013   0.002   TRP C 296 
 HIS   0.004   0.001   HIS F 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8418)
  covalent geometry    : angle       0.95024 (11490)
  hydrogen bonds       : bond        0.02790 (  220)
  hydrogen bonds       : angle       6.28386 (  537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.16 seconds
wall clock time: 34 minutes 53.37 seconds (2093.37 seconds total)