Starting phenix.real_space_refine
on Wed Feb  4 06:41:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vxv_43641/02_2026/8vxv_43641.map"
  }
  resolution = 3.7
  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=   0.002 sd=   0.018
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      66      5.16       5
     C    5814      2.51       5
     N    1584      2.21       5
     O    1680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9144
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1524
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 187}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 36
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.40, per 1000 atoms: 0.15
  Number of scatterers: 9144
  At special positions: 0
  Unit cell: (118.678, 109.074, 72.03, 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      66     16.00
     O    1680      8.00
     N    1584      7.00
     C    5814      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: 0.75
  Conformation dependent library (CDL) restraints added in 358.2 milliseconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      78.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A  44 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR A  54 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 84
      removed outlier: 3.679A  pdb=" N   LEU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 125 through 146
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 3.836A  pdb=" N   LYS A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU A 190 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'B' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU B  20 " --> pdb=" O   SER B  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA B  22 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET B  39 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR B  54 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 84
      removed outlier: 3.678A  pdb=" N   LEU B  69 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 110 through 120
    Processing helix  chain 'B' and resid 125 through 146
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.835A  pdb=" N   LYS B 170 " --> pdb=" O   ASP B 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 174 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU B 175 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 206
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'C' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU C  20 " --> pdb=" O   SER C  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA C  22 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET C  39 " --> pdb=" O   GLU C  35 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C  44 " --> pdb=" O   PHE C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR C  54 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 84
      removed outlier: 3.679A  pdb=" N   LEU C  69 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 110 through 120
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'C' and resid 160 through 175
      removed outlier: 3.835A  pdb=" N   LYS C 170 " --> pdb=" O   ASP C 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA C 174 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU C 175 " --> pdb=" O   THR C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU C 190 " --> pdb=" O   THR C 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL C 191 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 206
    Processing helix  chain 'C' and resid 210 through 218
    Processing helix  chain 'D' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU D  20 " --> pdb=" O   SER D  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA D  22 " --> pdb=" O   LEU D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 84
      removed outlier: 3.679A  pdb=" N   LEU D  69 " --> pdb=" O   ALA D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 105
    Processing helix  chain 'D' and resid 110 through 120
    Processing helix  chain 'D' and resid 125 through 146
    Processing helix  chain 'D' and resid 149 through 153
    Processing helix  chain 'D' and resid 160 through 175
      removed outlier: 3.836A  pdb=" N   LYS D 170 " --> pdb=" O   ASP D 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA D 174 " --> pdb=" O   LYS D 170 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU D 175 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU D 190 " --> pdb=" O   THR D 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL D 191 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 206
    Processing helix  chain 'D' and resid 210 through 218
    Processing helix  chain 'E' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU E  20 " --> pdb=" O   SER E  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA E  22 " --> pdb=" O   LEU E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER E  44 " --> pdb=" O   PHE E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR E  54 " --> pdb=" O   GLN E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 84
      removed outlier: 3.678A  pdb=" N   LEU E  69 " --> pdb=" O   ALA E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 105
    Processing helix  chain 'E' and resid 110 through 120
    Processing helix  chain 'E' and resid 125 through 146
    Processing helix  chain 'E' and resid 149 through 153
    Processing helix  chain 'E' and resid 160 through 175
      removed outlier: 3.835A  pdb=" N   LYS E 170 " --> pdb=" O   ASP E 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA E 174 " --> pdb=" O   LYS E 170 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU E 175 " --> pdb=" O   THR E 171 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU E 190 " --> pdb=" O   THR E 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL E 191 " --> pdb=" O   GLU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 206
    Processing helix  chain 'E' and resid 210 through 218
    Processing helix  chain 'F' and resid 16 through 31
      removed outlier: 3.576A  pdb=" N   LEU F  20 " --> pdb=" O   SER F  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA F  22 " --> pdb=" O   LEU F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
      removed outlier: 3.574A  pdb=" N   MET F  39 " --> pdb=" O   GLU F  35 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER F  44 " --> pdb=" O   PHE F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 58
      removed outlier: 3.742A  pdb=" N   THR F  54 " --> pdb=" O   GLN F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 84
      removed outlier: 3.679A  pdb=" N   LEU F  69 " --> pdb=" O   ALA F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 105
    Processing helix  chain 'F' and resid 110 through 120
    Processing helix  chain 'F' and resid 125 through 146
    Processing helix  chain 'F' and resid 149 through 153
    Processing helix  chain 'F' and resid 160 through 175
      removed outlier: 3.835A  pdb=" N   LYS F 170 " --> pdb=" O   ASP F 166 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA F 174 " --> pdb=" O   LYS F 170 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU F 175 " --> pdb=" O   THR F 171 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 193
      removed outlier: 4.147A  pdb=" N   LEU F 190 " --> pdb=" O   THR F 186 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL F 191 " --> pdb=" O   GLU F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 195 through 206
    Processing helix  chain 'F' and resid 210 through 218

    594 hydrogen bonds defined for protein.
    1746 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: 1.07

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3006
        1.34 -     1.46: 1576
        1.46 -     1.57: 4640
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 9342
  Sorted by residual:
  bond pdb=" CB  ARG E 132 "
       pdb=" CG  ARG E 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.24e-01
  bond pdb=" CB  ARG B 132 "
       pdb=" CG  ARG B 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.24e-01
  bond pdb=" CB  ARG C 132 "
       pdb=" CG  ARG C 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.05e-01
  bond pdb=" CB  ARG F 132 "
       pdb=" CG  ARG F 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.05e-01
  bond pdb=" CB  ARG A 132 "
       pdb=" CG  ARG A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.87e-01
  ... (remaining 9337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 11792
        1.08 -     2.16: 737
        2.16 -     3.24: 125
        3.24 -     4.33: 36
        4.33 -     5.41: 42
  Bond angle restraints: 12732
  Sorted by residual:
  angle pdb=" N   GLY A 206 "
        pdb=" CA  GLY A 206 "
        pdb=" C   GLY A 206 "
      ideal   model   delta    sigma   weight residual
     112.34  117.19   -4.85 2.04e+00 2.40e-01 5.65e+00
  angle pdb=" N   GLY D 206 "
        pdb=" CA  GLY D 206 "
        pdb=" C   GLY D 206 "
      ideal   model   delta    sigma   weight residual
     112.34  117.19   -4.85 2.04e+00 2.40e-01 5.65e+00
  angle pdb=" N   GLY F 206 "
        pdb=" CA  GLY F 206 "
        pdb=" C   GLY F 206 "
      ideal   model   delta    sigma   weight residual
     112.34  117.17   -4.83 2.04e+00 2.40e-01 5.61e+00
  angle pdb=" N   GLY C 206 "
        pdb=" CA  GLY C 206 "
        pdb=" C   GLY C 206 "
      ideal   model   delta    sigma   weight residual
     112.34  117.17   -4.83 2.04e+00 2.40e-01 5.61e+00
  angle pdb=" N   GLY B 206 "
        pdb=" CA  GLY B 206 "
        pdb=" C   GLY B 206 "
      ideal   model   delta    sigma   weight residual
     112.34  117.16   -4.82 2.04e+00 2.40e-01 5.58e+00
  ... (remaining 12727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 5232
       17.25 -    34.51: 252
       34.51 -    51.76: 114
       51.76 -    69.02: 30
       69.02 -    86.27: 18
  Dihedral angle restraints: 5646
    sinusoidal: 2166
      harmonic: 3480
  Sorted by residual:
  dihedral pdb=" CB  MET E 215 "
           pdb=" CG  MET E 215 "
           pdb=" SD  MET E 215 "
           pdb=" CE  MET E 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.97   59.03     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET B 215 "
           pdb=" CG  MET B 215 "
           pdb=" SD  MET B 215 "
           pdb=" CE  MET B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.97   59.03     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET D 215 "
           pdb=" CG  MET D 215 "
           pdb=" SD  MET D 215 "
           pdb=" CE  MET D 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    1.00   59.00     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 826
       0.030 -    0.060: 428
       0.060 -    0.090: 135
       0.090 -    0.120: 55
       0.120 -    0.150: 38
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CB  VAL F 126 "
            pdb=" CA  VAL F 126 "
            pdb=" CG1 VAL F 126 "
            pdb=" CG2 VAL F 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CB  VAL C 126 "
            pdb=" CA  VAL C 126 "
            pdb=" CG1 VAL C 126 "
            pdb=" CG2 VAL C 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CB  VAL B 126 "
            pdb=" CA  VAL B 126 "
            pdb=" CG1 VAL B 126 "
            pdb=" CG2 VAL B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.55e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1626
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 124 "   -0.064 5.00e-02 4.00e+02   9.72e-02 1.51e+01
        pdb=" N   PRO F 125 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO F 125 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO F 125 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 124 "    0.064 5.00e-02 4.00e+02   9.72e-02 1.51e+01
        pdb=" N   PRO C 125 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO C 125 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO C 125 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 124 "   -0.064 5.00e-02 4.00e+02   9.72e-02 1.51e+01
        pdb=" N   PRO E 125 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO E 125 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO E 125 "   -0.052 5.00e-02 4.00e+02
  ... (remaining 1623 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2184
        2.80 -     3.33: 9454
        3.33 -     3.85: 14604
        3.85 -     4.38: 15202
        4.38 -     4.90: 26587
  Nonbonded interactions: 68031
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 169 "
            pdb=" OG1 THR B 186 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR E 169 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR A 169 "
            pdb=" OG1 THR A 186 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR D 169 "
            pdb=" OG1 THR D 186 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR F 169 "
            pdb=" OG1 THR F 186 "
     model   vdw
     2.278 3.040
  ... (remaining 68026 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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 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:             1.950
  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:          0.200
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.970
  Find NCS groups from input model:        0.080
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9342  Z= 0.170
  Angle     :  0.664   5.408  12732  Z= 0.343
  Chirality :  0.045   0.150   1482
  Planarity :  0.007   0.097   1626
  Dihedral  : 13.921  86.273   3378
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.05 (0.26), residues: 1170
  helix:  1.22 (0.18), residues: 876
  sheet:  None (None), residues: 0
  loop : -0.78 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 143 
 TYR   0.029   0.003   TYR F 169 
 PHE   0.007   0.002   PHE F  40 
 TRP   0.022   0.002   TRP B 133 
 HIS   0.003   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 9342)
  covalent geometry    : angle       0.66423 (12732)
  hydrogen bonds       : bond        0.15921 (  594)
  hydrogen bonds       : angle       6.08132 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7067 (mmt90)
REVERT: A  155 GLN cc_start: 0.7692 (tt0) cc_final: 0.7384 (tt0)
REVERT: A  183 ASN cc_start: 0.9069 (m-40) cc_final: 0.8825 (m110)
REVERT: A  192 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8557 (mm-40)
REVERT: B   44 SER cc_start: 0.8872 (p) cc_final: 0.8574 (p)
REVERT: B  155 GLN cc_start: 0.7680 (tt0) cc_final: 0.7423 (tt0)
REVERT: C   44 SER cc_start: 0.8831 (p) cc_final: 0.8616 (p)
REVERT: C  103 ASP cc_start: 0.8553 (m-30) cc_final: 0.8297 (t0)
REVERT: C  154 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7621 (mtp85)
REVERT: C  155 GLN cc_start: 0.7752 (tt0) cc_final: 0.7440 (tt0)
REVERT: D  100 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7071 (mmt90)
REVERT: D  155 GLN cc_start: 0.7696 (tt0) cc_final: 0.7390 (tt0)
REVERT: D  183 ASN cc_start: 0.9074 (m-40) cc_final: 0.8832 (m110)
REVERT: D  192 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8554 (mm-40)
REVERT: E   44 SER cc_start: 0.8873 (p) cc_final: 0.8585 (p)
REVERT: E  155 GLN cc_start: 0.7682 (tt0) cc_final: 0.7429 (tt0)
REVERT: F   44 SER cc_start: 0.8840 (p) cc_final: 0.8624 (p)
REVERT: F  103 ASP cc_start: 0.8558 (m-30) cc_final: 0.8293 (t0)
REVERT: F  154 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7623 (mtp85)
REVERT: F  155 GLN cc_start: 0.7756 (tt0) cc_final: 0.7445 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.1214
  time to fit residues: 48.4639
Evaluate side-chains
  258 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
B  67 GLN
B 183 ASN
D  67 GLN
E  67 GLN
E 183 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.139518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.097120 restraints weight = 13750.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.100798 restraints weight = 8357.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.103176 restraints weight = 6259.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104497 restraints weight = 5275.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.105467 restraints weight = 4778.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9342  Z= 0.138
  Angle     :  0.565   5.940  12732  Z= 0.291
  Chirality :  0.039   0.124   1482
  Planarity :  0.006   0.061   1626
  Dihedral  :  3.665  12.393   1266
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 12.31 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.19 (0.25), residues: 1170
  helix:  1.28 (0.18), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.61 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  82 
 TYR   0.027   0.003   TYR A 169 
 PHE   0.005   0.001   PHE A  40 
 TRP   0.008   0.001   TRP F 133 
 HIS   0.001   0.000   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9342)
  covalent geometry    : angle       0.56496 (12732)
  hydrogen bonds       : bond        0.04366 (  594)
  hydrogen bonds       : angle       4.35397 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 286
  time to evaluate  : 0.383 
Fit side-chains
REVERT: B   44 SER cc_start: 0.9118 (p) cc_final: 0.8917 (p)
REVERT: B  154 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7766 (mtp85)
REVERT: C   44 SER cc_start: 0.9008 (p) cc_final: 0.8801 (p)
REVERT: C  103 ASP cc_start: 0.8588 (m-30) cc_final: 0.8240 (t0)
REVERT: C  183 ASN cc_start: 0.9021 (m-40) cc_final: 0.8735 (m110)
REVERT: E   44 SER cc_start: 0.9113 (p) cc_final: 0.8912 (p)
REVERT: E  154 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7766 (mtp85)
REVERT: F   44 SER cc_start: 0.9014 (p) cc_final: 0.8805 (p)
REVERT: F  103 ASP cc_start: 0.8591 (m-30) cc_final: 0.8233 (t0)
REVERT: F  183 ASN cc_start: 0.9028 (m-40) cc_final: 0.8741 (m110)
  outliers start: 8
  outliers final: 2
  residues processed: 288
  average time/residue: 0.1214
  time to fit residues: 45.6780
Evaluate side-chains
  252 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 250
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain D residue   18 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0070
   chunk 67 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 183 ASN
B  67 GLN
C  67 GLN
D  67 GLN
D 183 ASN
E  67 GLN
F  67 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.141654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.099680 restraints weight = 13572.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.103145 restraints weight = 8544.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.105439 restraints weight = 6496.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106851 restraints weight = 5512.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.107576 restraints weight = 4994.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   9342  Z= 0.113
  Angle     :  0.532   6.726  12732  Z= 0.266
  Chirality :  0.038   0.122   1482
  Planarity :  0.005   0.045   1626
  Dihedral  :  3.581  11.639   1266
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.71 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.20 (0.26), residues: 1170
  helix:  1.28 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.58 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 154 
 TYR   0.028   0.002   TYR A 169 
 PHE   0.007   0.001   PHE B 168 
 TRP   0.010   0.001   TRP D 133 
 HIS   0.001   0.000   HIS C  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9342)
  covalent geometry    : angle       0.53245 (12732)
  hydrogen bonds       : bond        0.03768 (  594)
  hydrogen bonds       : angle       4.07696 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 306
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8465 (m-30) cc_final: 0.8190 (t0)
REVERT: A  197 ASP cc_start: 0.8403 (p0) cc_final: 0.8166 (p0)
REVERT: B  103 ASP cc_start: 0.8482 (m-30) cc_final: 0.8109 (t70)
REVERT: B  154 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7731 (mtm-85)
REVERT: B  192 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8141 (mm-40)
REVERT: C  103 ASP cc_start: 0.8486 (m-30) cc_final: 0.8119 (t0)
REVERT: C  183 ASN cc_start: 0.9052 (m-40) cc_final: 0.8806 (m110)
REVERT: D  103 ASP cc_start: 0.8466 (m-30) cc_final: 0.8184 (t0)
REVERT: D  197 ASP cc_start: 0.8404 (p0) cc_final: 0.8168 (p0)
REVERT: E  103 ASP cc_start: 0.8476 (m-30) cc_final: 0.8106 (t70)
REVERT: E  154 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7725 (mtm-85)
REVERT: E  192 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8132 (mm-40)
REVERT: F   44 SER cc_start: 0.8928 (p) cc_final: 0.8728 (p)
REVERT: F  103 ASP cc_start: 0.8492 (m-30) cc_final: 0.8108 (t0)
REVERT: F  183 ASN cc_start: 0.9053 (m-40) cc_final: 0.8803 (m110)
  outliers start: 18
  outliers final: 2
  residues processed: 320
  average time/residue: 0.1086
  time to fit residues: 46.2748
Evaluate side-chains
  262 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 260
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0070
   chunk 48 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7400

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.141286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099216 restraints weight = 13846.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102635 restraints weight = 8677.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.104914 restraints weight = 6610.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.106160 restraints weight = 5608.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.107187 restraints weight = 5098.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9342  Z= 0.113
  Angle     :  0.535   6.609  12732  Z= 0.266
  Chirality :  0.038   0.119   1482
  Planarity :  0.005   0.042   1626
  Dihedral  :  3.506  12.467   1266
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 19.85 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.25 (0.26), residues: 1170
  helix:  1.32 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.58 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  82 
 TYR   0.023   0.003   TYR B 169 
 PHE   0.008   0.001   PHE E 168 
 TRP   0.009   0.001   TRP E 117 
 HIS   0.003   0.000   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9342)
  covalent geometry    : angle       0.53535 (12732)
  hydrogen bonds       : bond        0.03618 (  594)
  hydrogen bonds       : angle       3.93724 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 288
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.6952 (mmt90) cc_final: 0.6487 (mmt90)
REVERT: A  103 ASP cc_start: 0.8481 (m-30) cc_final: 0.8145 (t0)
REVERT: A  197 ASP cc_start: 0.8426 (p0) cc_final: 0.8190 (p0)
REVERT: B  103 ASP cc_start: 0.8434 (m-30) cc_final: 0.8085 (t0)
REVERT: C  103 ASP cc_start: 0.8395 (m-30) cc_final: 0.8069 (t0)
REVERT: C  183 ASN cc_start: 0.9051 (m-40) cc_final: 0.8806 (m110)
REVERT: D  100 ARG cc_start: 0.6941 (mmt90) cc_final: 0.6472 (mmt90)
REVERT: D  103 ASP cc_start: 0.8478 (m-30) cc_final: 0.8128 (t0)
REVERT: D  197 ASP cc_start: 0.8435 (p0) cc_final: 0.8200 (p0)
REVERT: E  103 ASP cc_start: 0.8424 (m-30) cc_final: 0.8080 (t0)
REVERT: F  103 ASP cc_start: 0.8397 (m-30) cc_final: 0.8061 (t0)
REVERT: F  183 ASN cc_start: 0.9050 (m-40) cc_final: 0.8803 (m110)
  outliers start: 10
  outliers final: 6
  residues processed: 296
  average time/residue: 0.1135
  time to fit residues: 44.5230
Evaluate side-chains
  280 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 274
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  185 MET
Chi-restraints excluded: chain E residue  171 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    0.2980
   chunk 89 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 47 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 219 GLN
C 219 GLN
E 219 GLN
F 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.138214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094493 restraints weight = 13941.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097735 restraints weight = 9022.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099880 restraints weight = 6995.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.101154 restraints weight = 6018.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101643 restraints weight = 5516.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9342  Z= 0.136
  Angle     :  0.578  10.448  12732  Z= 0.281
  Chirality :  0.039   0.121   1482
  Planarity :  0.005   0.043   1626
  Dihedral  :  3.428  12.523   1266
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.38 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.52 (0.25), residues: 1170
  helix:  1.51 (0.18), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.45 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  82 
 TYR   0.017   0.002   TYR E 169 
 PHE   0.006   0.001   PHE C  40 
 TRP   0.008   0.001   TRP F 117 
 HIS   0.002   0.000   HIS D  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9342)
  covalent geometry    : angle       0.57832 (12732)
  hydrogen bonds       : bond        0.03800 (  594)
  hydrogen bonds       : angle       3.91347 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 294
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7249 (mmt90) cc_final: 0.6795 (mmt90)
REVERT: A  103 ASP cc_start: 0.8595 (m-30) cc_final: 0.8154 (t0)
REVERT: A  197 ASP cc_start: 0.8510 (p0) cc_final: 0.8278 (p0)
REVERT: B   79 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8525 (mm-30)
REVERT: B  103 ASP cc_start: 0.8445 (m-30) cc_final: 0.8086 (t0)
REVERT: C   50 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8426 (tp40)
REVERT: C  100 ARG cc_start: 0.7188 (mmt90) cc_final: 0.6828 (mmt90)
REVERT: C  103 ASP cc_start: 0.8501 (m-30) cc_final: 0.8142 (t0)
REVERT: C  183 ASN cc_start: 0.9068 (m-40) cc_final: 0.8819 (m110)
REVERT: D  100 ARG cc_start: 0.7244 (mmt90) cc_final: 0.6791 (mmt90)
REVERT: D  103 ASP cc_start: 0.8596 (m-30) cc_final: 0.8145 (t0)
REVERT: D  197 ASP cc_start: 0.8521 (p0) cc_final: 0.8290 (p0)
REVERT: E   79 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: E  103 ASP cc_start: 0.8449 (m-30) cc_final: 0.8093 (t0)
REVERT: F   50 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8427 (tp40)
REVERT: F  100 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6831 (mmt90)
REVERT: F  103 ASP cc_start: 0.8501 (m-30) cc_final: 0.8130 (t0)
REVERT: F  183 ASN cc_start: 0.9067 (m-40) cc_final: 0.8817 (m110)
  outliers start: 28
  outliers final: 20
  residues processed: 316
  average time/residue: 0.1046
  time to fit residues: 44.2927
Evaluate side-chains
  266 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 246
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain F residue  110 THR
Chi-restraints excluded: chain F residue  136 LEU
Chi-restraints excluded: chain F residue  191 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 219 GLN
B 155 GLN
C 219 GLN
D  67 GLN
D 219 GLN
E 155 GLN
F 219 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.139313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.096264 restraints weight = 13789.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099608 restraints weight = 8748.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.101791 restraints weight = 6698.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102871 restraints weight = 5711.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103943 restraints weight = 5227.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9342  Z= 0.135
  Angle     :  0.582   9.615  12732  Z= 0.288
  Chirality :  0.039   0.122   1482
  Planarity :  0.005   0.037   1626
  Dihedral  :  3.452  14.025   1266
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.02 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.63 (0.25), residues: 1170
  helix:  1.63 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.60 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  82 
 TYR   0.014   0.002   TYR B 169 
 PHE   0.006   0.001   PHE B 168 
 TRP   0.008   0.001   TRP D 117 
 HIS   0.001   0.000   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9342)
  covalent geometry    : angle       0.58233 (12732)
  hydrogen bonds       : bond        0.03758 (  594)
  hydrogen bonds       : angle       3.92290 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 274
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7321 (mmt90) cc_final: 0.6816 (mmt90)
REVERT: A  103 ASP cc_start: 0.8552 (m-30) cc_final: 0.8088 (t0)
REVERT: A  197 ASP cc_start: 0.8484 (p0) cc_final: 0.8250 (p0)
REVERT: B  103 ASP cc_start: 0.8417 (m-30) cc_final: 0.8067 (t0)
REVERT: C  100 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6916 (mmt90)
REVERT: C  103 ASP cc_start: 0.8482 (m-30) cc_final: 0.8151 (t0)
REVERT: C  130 TYR cc_start: 0.8812 (t80) cc_final: 0.8327 (t80)
REVERT: C  183 ASN cc_start: 0.9077 (m-40) cc_final: 0.8816 (m110)
REVERT: C  197 ASP cc_start: 0.8321 (p0) cc_final: 0.8110 (p0)
REVERT: D  100 ARG cc_start: 0.7326 (mmt90) cc_final: 0.6819 (mmt90)
REVERT: D  103 ASP cc_start: 0.8563 (m-30) cc_final: 0.8087 (t0)
REVERT: D  197 ASP cc_start: 0.8486 (p0) cc_final: 0.8253 (p0)
REVERT: E  103 ASP cc_start: 0.8418 (m-30) cc_final: 0.8068 (t0)
REVERT: F  100 ARG cc_start: 0.7264 (mmt90) cc_final: 0.6914 (mmt90)
REVERT: F  103 ASP cc_start: 0.8483 (m-30) cc_final: 0.8140 (t0)
REVERT: F  130 TYR cc_start: 0.8822 (t80) cc_final: 0.8319 (t80)
REVERT: F  183 ASN cc_start: 0.9076 (m-40) cc_final: 0.8812 (m110)
REVERT: F  197 ASP cc_start: 0.8316 (p0) cc_final: 0.8107 (p0)
  outliers start: 28
  outliers final: 18
  residues processed: 294
  average time/residue: 0.1148
  time to fit residues: 45.2131
Evaluate side-chains
  272 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 254
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain E residue   44 SER
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain F residue  110 THR
Chi-restraints excluded: chain F residue  191 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    0.4980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 155 GLN
E 155 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.139850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.096743 restraints weight = 14006.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.100232 restraints weight = 8691.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.102500 restraints weight = 6590.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.103862 restraints weight = 5594.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.104614 restraints weight = 5081.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9342  Z= 0.121
  Angle     :  0.585   9.417  12732  Z= 0.286
  Chirality :  0.038   0.124   1482
  Planarity :  0.005   0.037   1626
  Dihedral  :  3.470  15.985   1266
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 22.61 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.72 (0.25), residues: 1170
  helix:  1.65 (0.18), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.36 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  82 
 TYR   0.018   0.002   TYR E 169 
 PHE   0.007   0.001   PHE C 168 
 TRP   0.006   0.001   TRP E 117 
 HIS   0.002   0.000   HIS F  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9342)
  covalent geometry    : angle       0.58451 (12732)
  hydrogen bonds       : bond        0.03637 (  594)
  hydrogen bonds       : angle       3.93353 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 285
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8544 (m-30) cc_final: 0.8047 (t0)
REVERT: B  100 ARG cc_start: 0.6951 (mmt90) cc_final: 0.6560 (mmt90)
REVERT: B  103 ASP cc_start: 0.8392 (m-30) cc_final: 0.8040 (t70)
REVERT: C  100 ARG cc_start: 0.7215 (mmt90) cc_final: 0.6868 (mmt90)
REVERT: C  103 ASP cc_start: 0.8468 (m-30) cc_final: 0.8170 (t0)
REVERT: C  183 ASN cc_start: 0.9023 (m-40) cc_final: 0.8775 (m110)
REVERT: D  103 ASP cc_start: 0.8546 (m-30) cc_final: 0.8039 (t0)
REVERT: E  100 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6559 (mmt90)
REVERT: E  103 ASP cc_start: 0.8398 (m-30) cc_final: 0.8048 (t70)
REVERT: F  100 ARG cc_start: 0.7220 (mmt90) cc_final: 0.6869 (mmt90)
REVERT: F  103 ASP cc_start: 0.8466 (m-30) cc_final: 0.8159 (t0)
REVERT: F  183 ASN cc_start: 0.9026 (m-40) cc_final: 0.8776 (m110)
  outliers start: 16
  outliers final: 8
  residues processed: 297
  average time/residue: 0.1169
  time to fit residues: 45.9100
Evaluate side-chains
  269 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 261
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain F residue  110 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0570
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 219 GLN
B 155 GLN
C 219 GLN
D  67 GLN
D 219 GLN
E 155 GLN
F 219 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.095135 restraints weight = 13797.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098578 restraints weight = 8582.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.100800 restraints weight = 6522.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.101915 restraints weight = 5547.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.102964 restraints weight = 5067.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9342  Z= 0.161
  Angle     :  0.646   8.682  12732  Z= 0.324
  Chirality :  0.042   0.275   1482
  Planarity :  0.005   0.037   1626
  Dihedral  :  3.532  19.256   1266
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.25 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.67 (0.25), residues: 1170
  helix:  1.61 (0.18), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.36 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  82 
 TYR   0.014   0.002   TYR E 169 
 PHE   0.006   0.001   PHE F  40 
 TRP   0.009   0.001   TRP E 117 
 HIS   0.001   0.000   HIS E  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9342)
  covalent geometry    : angle       0.64617 (12732)
  hydrogen bonds       : bond        0.03999 (  594)
  hydrogen bonds       : angle       4.09020 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 269
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8603 (m-30) cc_final: 0.8060 (t0)
REVERT: B  103 ASP cc_start: 0.8456 (m-30) cc_final: 0.8069 (t0)
REVERT: C  100 ARG cc_start: 0.7420 (mmt90) cc_final: 0.7011 (mmt90)
REVERT: C  103 ASP cc_start: 0.8500 (m-30) cc_final: 0.8163 (t0)
REVERT: C  130 TYR cc_start: 0.8791 (t80) cc_final: 0.8275 (t80)
REVERT: C  183 ASN cc_start: 0.9035 (m-40) cc_final: 0.8761 (m110)
REVERT: D  103 ASP cc_start: 0.8620 (m-30) cc_final: 0.8063 (t0)
REVERT: E  103 ASP cc_start: 0.8460 (m-30) cc_final: 0.8083 (t0)
REVERT: F  100 ARG cc_start: 0.7428 (mmt90) cc_final: 0.7014 (mmt90)
REVERT: F  103 ASP cc_start: 0.8500 (m-30) cc_final: 0.8157 (t0)
REVERT: F  130 TYR cc_start: 0.8797 (t80) cc_final: 0.8266 (t80)
REVERT: F  183 ASN cc_start: 0.9035 (m-40) cc_final: 0.8757 (m110)
  outliers start: 22
  outliers final: 16
  residues processed: 283
  average time/residue: 0.1114
  time to fit residues: 42.2896
Evaluate side-chains
  281 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 265
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 LEU
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain E residue  136 LEU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain F residue  110 THR
Chi-restraints excluded: chain F residue  191 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0270
   chunk 29 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 119 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
B 155 GLN
B 219 GLN
C 219 GLN
D 219 GLN
E 155 GLN
** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 219 GLN
F 219 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.097676 restraints weight = 13690.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101100 restraints weight = 8647.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.103324 restraints weight = 6616.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.104732 restraints weight = 5646.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.105526 restraints weight = 5149.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9342  Z= 0.129
  Angle     :  0.635  11.888  12732  Z= 0.314
  Chirality :  0.040   0.181   1482
  Planarity :  0.005   0.038   1626
  Dihedral  :  3.611  20.973   1266
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 23.89 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.59 (0.25), residues: 1170
  helix:  1.54 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.35 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  82 
 TYR   0.016   0.002   TYR E 169 
 PHE   0.009   0.001   PHE F 168 
 TRP   0.010   0.001   TRP E 117 
 HIS   0.001   0.000   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9342)
  covalent geometry    : angle       0.63470 (12732)
  hydrogen bonds       : bond        0.03688 (  594)
  hydrogen bonds       : angle       4.09457 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 277
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8492 (m-30) cc_final: 0.7962 (t0)
REVERT: A  126 VAL cc_start: 0.8911 (m) cc_final: 0.8652 (p)
REVERT: B  100 ARG cc_start: 0.7126 (mmt90) cc_final: 0.6750 (mmt90)
REVERT: B  103 ASP cc_start: 0.8324 (m-30) cc_final: 0.7789 (t0)
REVERT: B  118 MET cc_start: 0.7814 (mmm) cc_final: 0.7336 (mmt)
REVERT: C  100 ARG cc_start: 0.7291 (mmt90) cc_final: 0.6972 (mmt90)
REVERT: C  103 ASP cc_start: 0.8400 (m-30) cc_final: 0.8147 (t0)
REVERT: C  130 TYR cc_start: 0.8769 (t80) cc_final: 0.8330 (t80)
REVERT: C  183 ASN cc_start: 0.8986 (m-40) cc_final: 0.8733 (m110)
REVERT: D  103 ASP cc_start: 0.8514 (m-30) cc_final: 0.7963 (t0)
REVERT: D  126 VAL cc_start: 0.8909 (m) cc_final: 0.8648 (p)
REVERT: E  100 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6741 (mmt90)
REVERT: E  103 ASP cc_start: 0.8313 (m-30) cc_final: 0.7796 (t0)
REVERT: E  118 MET cc_start: 0.7821 (mmm) cc_final: 0.7341 (mmt)
REVERT: F  100 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6969 (mmt90)
REVERT: F  103 ASP cc_start: 0.8394 (m-30) cc_final: 0.8141 (t0)
REVERT: F  130 TYR cc_start: 0.8778 (t80) cc_final: 0.8328 (t80)
REVERT: F  183 ASN cc_start: 0.8993 (m-40) cc_final: 0.8736 (m110)
  outliers start: 15
  outliers final: 3
  residues processed: 288
  average time/residue: 0.1148
  time to fit residues: 43.7064
Evaluate side-chains
  265 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 262
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue  110 THR
Chi-restraints excluded: chain F residue  191 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0050
   chunk 105 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
B 219 GLN
C 219 GLN
D 219 GLN
E 219 GLN
F 219 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.140891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098137 restraints weight = 13689.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.101539 restraints weight = 8684.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.103642 restraints weight = 6695.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.105041 restraints weight = 5740.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.105720 restraints weight = 5240.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9342  Z= 0.133
  Angle     :  0.645  11.949  12732  Z= 0.323
  Chirality :  0.040   0.169   1482
  Planarity :  0.005   0.037   1626
  Dihedral  :  3.661  21.897   1266
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 25.58 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.25), residues: 1170
  helix:  1.50 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.32 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  82 
 TYR   0.013   0.002   TYR E 169 
 PHE   0.007   0.001   PHE B 168 
 TRP   0.008   0.001   TRP E 117 
 HIS   0.002   0.000   HIS D  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9342)
  covalent geometry    : angle       0.64534 (12732)
  hydrogen bonds       : bond        0.03695 (  594)
  hydrogen bonds       : angle       4.11980 ( 1746)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 278
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8505 (m-30) cc_final: 0.7964 (t0)
REVERT: A  126 VAL cc_start: 0.8915 (m) cc_final: 0.8658 (p)
REVERT: B   80 TRP cc_start: 0.8836 (t-100) cc_final: 0.8377 (t-100)
REVERT: B  100 ARG cc_start: 0.7156 (mmt90) cc_final: 0.6635 (mmt90)
REVERT: B  103 ASP cc_start: 0.8307 (m-30) cc_final: 0.7785 (t0)
REVERT: B  118 MET cc_start: 0.7828 (mmm) cc_final: 0.7372 (mmt)
REVERT: C  130 TYR cc_start: 0.8790 (t80) cc_final: 0.8384 (t80)
REVERT: C  183 ASN cc_start: 0.8995 (m-40) cc_final: 0.8737 (m110)
REVERT: D  103 ASP cc_start: 0.8517 (m-30) cc_final: 0.7960 (t0)
REVERT: D  126 VAL cc_start: 0.8909 (m) cc_final: 0.8651 (p)
REVERT: E   80 TRP cc_start: 0.8841 (t-100) cc_final: 0.8387 (t-100)
REVERT: E  100 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6622 (mmt90)
REVERT: E  103 ASP cc_start: 0.8294 (m-30) cc_final: 0.7790 (t0)
REVERT: E  118 MET cc_start: 0.7837 (mmm) cc_final: 0.7381 (mmt)
REVERT: F  130 TYR cc_start: 0.8790 (t80) cc_final: 0.8366 (t80)
REVERT: F  183 ASN cc_start: 0.8995 (m-40) cc_final: 0.8726 (m110)
  outliers start: 10
  outliers final: 6
  residues processed: 282
  average time/residue: 0.1078
  time to fit residues: 40.5427
Evaluate side-chains
  272 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 266
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain D residue  219 GLN
Chi-restraints excluded: chain E residue  219 GLN
Chi-restraints excluded: chain F residue  110 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    0.0030
   chunk 91 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 108 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 219 GLN
B  67 GLN
B 155 GLN
B 219 GLN
D  67 GLN
D 219 GLN
E  67 GLN
E 155 GLN
E 219 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.141767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099608 restraints weight = 13548.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.103001 restraints weight = 8562.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.105211 restraints weight = 6547.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.106619 restraints weight = 5592.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.107225 restraints weight = 5091.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9342  Z= 0.132
  Angle     :  0.671  11.951  12732  Z= 0.323
  Chirality :  0.040   0.229   1482
  Planarity :  0.005   0.038   1626
  Dihedral  :  3.655  17.805   1266
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 26.11 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.56 (0.25), residues: 1170
  helix:  1.51 (0.18), residues: 882
  sheet:  None (None), residues: 0
  loop : -0.32 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  82 
 TYR   0.030   0.003   TYR A 169 
 PHE   0.009   0.001   PHE C 168 
 TRP   0.008   0.001   TRP E 117 
 HIS   0.001   0.000   HIS E  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9342)
  covalent geometry    : angle       0.67052 (12732)
  hydrogen bonds       : bond        0.03672 (  594)
  hydrogen bonds       : angle       4.24214 ( 1746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2197.42 seconds
wall clock time: 38 minutes 24.29 seconds (2304.29 seconds total)