Starting phenix.real_space_refine
on Tue Mar  3 20:51:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2026/7b03_11955.cif"
  }
  resolution = 2.93
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.442
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      55      5.16       5
     C    5855      2.51       5
     N    1290      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8670
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1714
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 5, 'TRANS': 211}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.27, per 1000 atoms: 0.15
  Number of scatterers: 8670
  At special positions: 0
  Unit cell: (103.2, 100.62, 67.08, 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      55     16.00
     O    1470      8.00
     N    1290      7.00
     C    5855      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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 313.8 milliseconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2000

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 0 sheets defined
      89.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 53
      removed outlier: 3.784A  pdb=" N   ARG A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ASP A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 87
      removed outlier: 3.670A  pdb=" N   TYR A  79 " --> pdb=" O   TRP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 118
      Proline residue:  A 104  - end of helix
      removed outlier: 4.214A  pdb=" N   PHE A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TYR A 111 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 144
    Processing helix  chain 'A' and resid 148 through 177
      removed outlier: 3.824A  pdb=" N   GLY A 170 " --> pdb=" O   GLU A 166 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLU A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LYS A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 208
      removed outlier: 3.945A  pdb=" N   TRP A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A 200 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   TYR A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
    Processing helix  chain 'A' and resid 219 through 249
      removed outlier: 3.516A  pdb=" N   LEU A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   PHE A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 53
      removed outlier: 3.783A  pdb=" N   ARG B  52 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ASP B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 87
      removed outlier: 3.671A  pdb=" N   TYR B  79 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 118
      Proline residue:  B 104  - end of helix
      removed outlier: 4.214A  pdb=" N   PHE B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TYR B 111 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 144
    Processing helix  chain 'B' and resid 148 through 177
      removed outlier: 3.823A  pdb=" N   GLY B 170 " --> pdb=" O   GLU B 166 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   GLU B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY B 172 " --> pdb=" O   TRP B 168 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LYS B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 208
      removed outlier: 3.945A  pdb=" N   TRP B 198 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA B 199 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 200 " --> pdb=" O   PHE B 196 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR B 201 " --> pdb=" O   GLY B 197 " (cutoff:3.500A)
      Proline residue:  B 202  - end of helix
    Processing helix  chain 'B' and resid 219 through 249
      removed outlier: 3.516A  pdb=" N   LEU B 234 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   PHE B 235 " --> pdb=" O   ASN B 231 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 53
      removed outlier: 3.783A  pdb=" N   ARG C  52 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ASP C  53 " --> pdb=" O   PHE C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 87
      removed outlier: 3.670A  pdb=" N   TYR C  79 " --> pdb=" O   TRP C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 118
      Proline residue:  C 104  - end of helix
      removed outlier: 4.214A  pdb=" N   PHE C 110 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TYR C 111 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 144
    Processing helix  chain 'C' and resid 148 through 177
      removed outlier: 3.824A  pdb=" N   GLY C 170 " --> pdb=" O   GLU C 166 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLU C 171 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY C 172 " --> pdb=" O   TRP C 168 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LYS C 173 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 208
      removed outlier: 3.945A  pdb=" N   TRP C 198 " --> pdb=" O   ILE C 194 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA C 199 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE C 200 " --> pdb=" O   PHE C 196 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR C 201 " --> pdb=" O   GLY C 197 " (cutoff:3.500A)
      Proline residue:  C 202  - end of helix
    Processing helix  chain 'C' and resid 219 through 249
      removed outlier: 3.515A  pdb=" N   LEU C 234 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   PHE C 235 " --> pdb=" O   ASN C 231 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY C 236 " --> pdb=" O   LYS C 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 53
      removed outlier: 3.784A  pdb=" N   ARG D  52 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ASP D  53 " --> pdb=" O   PHE D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 87
      removed outlier: 3.669A  pdb=" N   TYR D  79 " --> pdb=" O   TRP D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 118
      Proline residue:  D 104  - end of helix
      removed outlier: 4.214A  pdb=" N   PHE D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TYR D 111 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 144
    Processing helix  chain 'D' and resid 148 through 177
      removed outlier: 3.824A  pdb=" N   GLY D 170 " --> pdb=" O   GLU D 166 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   GLU D 171 " --> pdb=" O   LEU D 167 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY D 172 " --> pdb=" O   TRP D 168 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LYS D 173 " --> pdb=" O   ALA D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 208
      removed outlier: 3.945A  pdb=" N   TRP D 198 " --> pdb=" O   ILE D 194 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA D 199 " --> pdb=" O   ILE D 195 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ILE D 200 " --> pdb=" O   PHE D 196 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR D 201 " --> pdb=" O   GLY D 197 " (cutoff:3.500A)
      Proline residue:  D 202  - end of helix
    Processing helix  chain 'D' and resid 219 through 249
      removed outlier: 3.516A  pdb=" N   LEU D 234 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   PHE D 235 " --> pdb=" O   ASN D 231 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY D 236 " --> pdb=" O   LYS D 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 53
      removed outlier: 3.783A  pdb=" N   ARG E  52 " --> pdb=" O   PHE E  48 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ASP E  53 " --> pdb=" O   PHE E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 87
      removed outlier: 3.670A  pdb=" N   TYR E  79 " --> pdb=" O   TRP E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 118
      Proline residue:  E 104  - end of helix
      removed outlier: 4.214A  pdb=" N   PHE E 110 " --> pdb=" O   LEU E 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TYR E 111 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 144
    Processing helix  chain 'E' and resid 148 through 177
      removed outlier: 3.824A  pdb=" N   GLY E 170 " --> pdb=" O   GLU E 166 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   GLU E 171 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY E 172 " --> pdb=" O   TRP E 168 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LYS E 173 " --> pdb=" O   ALA E 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 208
      removed outlier: 3.945A  pdb=" N   TRP E 198 " --> pdb=" O   ILE E 194 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA E 199 " --> pdb=" O   ILE E 195 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE E 200 " --> pdb=" O   PHE E 196 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR E 201 " --> pdb=" O   GLY E 197 " (cutoff:3.500A)
      Proline residue:  E 202  - end of helix
    Processing helix  chain 'E' and resid 219 through 249
      removed outlier: 3.516A  pdb=" N   LEU E 234 " --> pdb=" O   VAL E 230 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   PHE E 235 " --> pdb=" O   ASN E 231 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY E 236 " --> pdb=" O   LYS E 232 " (cutoff:3.500A)

    720 hydrogen bonds defined for protein.
    2160 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: 1.22

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1288
        1.32 -     1.44: 2758
        1.44 -     1.57: 4789
        1.57 -     1.69: 0
        1.69 -     1.81: 95
  Bond restraints: 8930
  Sorted by residual:
  bond pdb=" C   TRP B  75 "
       pdb=" O   TRP B  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.039 1.15e-02 7.56e+03 1.12e+01
  bond pdb=" C   TRP A  75 "
       pdb=" O   TRP A  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.15e-02 7.56e+03 1.10e+01
  bond pdb=" C   TRP D  75 "
       pdb=" O   TRP D  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" C   TRP C  75 "
       pdb=" O   TRP C  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" C   TRP E  75 "
       pdb=" O   TRP E  75 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.038 1.15e-02 7.56e+03 1.07e+01
  ... (remaining 8925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 12120
        3.75 -     7.51: 50
        7.51 -    11.26: 10
       11.26 -    15.01: 5
       15.01 -    18.77: 10
  Bond angle restraints: 12195
  Sorted by residual:
  angle pdb=" C16 RET D 301 "
        pdb=" C1  RET D 301 "
        pdb=" C2  RET D 301 "
      ideal   model   delta    sigma   weight residual
     105.80  124.57  -18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" C16 RET B 301 "
        pdb=" C1  RET B 301 "
        pdb=" C2  RET B 301 "
      ideal   model   delta    sigma   weight residual
     105.80  124.55  -18.75 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" C16 RET A 301 "
        pdb=" C1  RET A 301 "
        pdb=" C2  RET A 301 "
      ideal   model   delta    sigma   weight residual
     105.80  124.53  -18.73 3.00e+00 1.11e-01 3.90e+01
  angle pdb=" C16 RET E 301 "
        pdb=" C1  RET E 301 "
        pdb=" C2  RET E 301 "
      ideal   model   delta    sigma   weight residual
     105.80  124.51  -18.71 3.00e+00 1.11e-01 3.89e+01
  angle pdb=" C16 RET C 301 "
        pdb=" C1  RET C 301 "
        pdb=" C2  RET C 301 "
      ideal   model   delta    sigma   weight residual
     105.80  124.51  -18.71 3.00e+00 1.11e-01 3.89e+01
  ... (remaining 12190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.03: 4795
       22.03 -    44.05: 115
       44.05 -    66.08: 20
       66.08 -    88.11: 10
       88.11 -   110.13: 10
  Dihedral angle restraints: 4950
    sinusoidal: 1805
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" C2  RET E 301 "
           pdb=" C3  RET E 301 "
           pdb=" C4  RET E 301 "
           pdb=" C5  RET E 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      42.40  -67.73  110.13     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" C2  RET A 301 "
           pdb=" C3  RET A 301 "
           pdb=" C4  RET A 301 "
           pdb=" C5  RET A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      42.40  -67.71  110.11     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" C2  RET D 301 "
           pdb=" C3  RET D 301 "
           pdb=" C4  RET D 301 "
           pdb=" C5  RET D 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      42.40  -67.70  110.10     1      3.00e+01 1.11e-03 1.43e+01
  ... (remaining 4947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 699
       0.026 -    0.051: 402
       0.051 -    0.077: 200
       0.077 -    0.102: 50
       0.102 -    0.128: 19
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CA  TYR E 201 "
            pdb=" N   TYR E 201 "
            pdb=" C   TYR E 201 "
            pdb=" CB  TYR E 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  TYR D 201 "
            pdb=" N   TYR D 201 "
            pdb=" C   TYR D 201 "
            pdb=" CB  TYR D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  TYR A 201 "
            pdb=" N   TYR A 201 "
            pdb=" C   TYR A 201 "
            pdb=" CB  TYR A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 1367 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E 229 "   -0.006 2.00e-02 2.50e+03   1.18e-02 1.40e+00
        pdb=" C   PHE E 229 "    0.020 2.00e-02 2.50e+03
        pdb=" O   PHE E 229 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL E 230 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 229 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.36e+00
        pdb=" C   PHE B 229 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   PHE B 229 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL B 230 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 229 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   PHE A 229 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   PHE A 229 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL A 230 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 548
        2.73 -     3.27: 9312
        3.27 -     3.82: 15340
        3.82 -     4.36: 17990
        4.36 -     4.90: 31016
  Nonbonded interactions: 74206
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E  77 "
            pdb=" OD2 ASP E 228 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OH  TYR C  77 "
            pdb=" OD2 ASP C 228 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OH  TYR B  77 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OH  TYR A  77 "
            pdb=" OD2 ASP A 228 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OH  TYR D  77 "
            pdb=" OD2 ASP D 228 "
     model   vdw
     2.191 3.040
  ... (remaining 74201 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.480
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
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      :  0.006   0.087   8935  Z= 0.343
  Angle     :  0.896  18.768  12195  Z= 0.411
  Chirality :  0.039   0.128   1370
  Planarity :  0.004   0.026   1450
  Dihedral  : 13.223 110.134   2950
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1065
  helix:  1.33 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -2.49 (0.37), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  52 
 TYR   0.009   0.001   TYR E 187 
 PHE   0.012   0.002   PHE E 235 
 TRP   0.011   0.001   TRP C 168 
 HIS   0.001   0.001   HIS E  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8930)
  covalent geometry    : angle       0.89638 (12195)
  hydrogen bonds       : bond        0.08731 (  720)
  hydrogen bonds       : angle       4.76206 ( 2160)
  Misc. bond           : bond        0.08707 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.6808 (m-30) cc_final: 0.6579 (m-30)
REVERT: A  163 MET cc_start: 0.8067 (mtp) cc_final: 0.7710 (mtp)
REVERT: A  192 TYR cc_start: 0.7791 (m-80) cc_final: 0.7449 (m-80)
REVERT: B  125 PHE cc_start: 0.8641 (t80) cc_final: 0.8388 (t80)
REVERT: B  163 MET cc_start: 0.8195 (mtp) cc_final: 0.7972 (mtp)
REVERT: B  191 MET cc_start: 0.8375 (ttm) cc_final: 0.8061 (ttp)
REVERT: C   80 MET cc_start: 0.6001 (mtm) cc_final: 0.5700 (mtm)
REVERT: C  138 PHE cc_start: 0.8509 (m-80) cc_final: 0.8203 (m-80)
REVERT: C  147 MET cc_start: 0.6964 (ttt) cc_final: 0.6648 (ttm)
REVERT: C  163 MET cc_start: 0.8090 (mtp) cc_final: 0.7609 (mtp)
REVERT: C  206 PHE cc_start: 0.8079 (t80) cc_final: 0.7812 (t80)
REVERT: D  141 MET cc_start: 0.8032 (mtp) cc_final: 0.7830 (ttm)
REVERT: E   80 MET cc_start: 0.6062 (mtm) cc_final: 0.5772 (mtp)
REVERT: E  141 MET cc_start: 0.8050 (mtp) cc_final: 0.7675 (mtm)
REVERT: E  192 TYR cc_start: 0.7434 (m-80) cc_final: 0.7090 (m-80)
  outliers start: 0
  outliers final: 1
  residues processed: 209
  average time/residue: 0.2813
  time to fit residues: 66.1143
Evaluate side-chains
  181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 225 ASN
B 241 ASN
C 177 ASN

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 = 0.162972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.137241 restraints weight = 9312.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.48
r_work: 0.3263 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8935  Z= 0.129
  Angle     :  0.479   5.738  12195  Z= 0.252
  Chirality :  0.036   0.112   1370
  Planarity :  0.003   0.027   1450
  Dihedral  : 10.697 111.875   1217
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  9.15 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.25), residues: 1065
  helix:  1.87 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -2.02 (0.46), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  52 
 TYR   0.010   0.001   TYR C 187 
 PHE   0.012   0.002   PHE D 235 
 TRP   0.011   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8930)
  covalent geometry    : angle       0.47868 (12195)
  hydrogen bonds       : bond        0.04628 (  720)
  hydrogen bonds       : angle       3.67659 ( 2160)
  Misc. bond           : bond        0.00026 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.6847 (t80)
REVERT: A   53 ASP cc_start: 0.7986 (m-30) cc_final: 0.7739 (m-30)
REVERT: B   34 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6919 (t80)
REVERT: B  125 PHE cc_start: 0.8438 (t80) cc_final: 0.8221 (t80)
REVERT: B  138 PHE cc_start: 0.8607 (m-80) cc_final: 0.8382 (OUTLIER)
REVERT: B  163 MET cc_start: 0.8460 (mtp) cc_final: 0.8231 (mtp)
REVERT: C   80 MET cc_start: 0.6693 (mtm) cc_final: 0.6362 (mtm)
REVERT: C  147 MET cc_start: 0.7157 (ttt) cc_final: 0.6746 (ttm)
REVERT: C  163 MET cc_start: 0.8248 (mtp) cc_final: 0.7766 (mtp)
REVERT: C  177 ASN cc_start: 0.8134 (m-40) cc_final: 0.7699 (m-40)
REVERT: C  192 TYR cc_start: 0.8526 (m-80) cc_final: 0.8110 (m-80)
REVERT: C  206 PHE cc_start: 0.8290 (t80) cc_final: 0.8040 (t80)
REVERT: D  138 PHE cc_start: 0.8472 (m-80) cc_final: 0.8247 (m-80)
REVERT: D  192 TYR cc_start: 0.8157 (m-80) cc_final: 0.7845 (m-80)
REVERT: E   80 MET cc_start: 0.6523 (mtm) cc_final: 0.6191 (mtp)
REVERT: E  141 MET cc_start: 0.8155 (mtp) cc_final: 0.7844 (ttm)
REVERT: E  191 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8216 (ttm)
  outliers start: 26
  outliers final: 17
  residues processed: 214
  average time/residue: 0.2757
  time to fit residues: 66.2940
Evaluate side-chains
  199 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 42 optimal weight:   50.0000
   chunk 6 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.160936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.136750 restraints weight = 9142.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.17
r_work: 0.3265 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8935  Z= 0.166
  Angle     :  0.525   7.862  12195  Z= 0.273
  Chirality :  0.038   0.113   1370
  Planarity :  0.004   0.030   1450
  Dihedral  : 10.406 109.914   1215
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 11.19 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.25), residues: 1065
  helix:  1.85 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.68 (0.50), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  52 
 TYR   0.013   0.001   TYR C 187 
 PHE   0.015   0.002   PHE D 125 
 TRP   0.011   0.001   TRP D 168 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8930)
  covalent geometry    : angle       0.52497 (12195)
  hydrogen bonds       : bond        0.05101 (  720)
  hydrogen bonds       : angle       3.68903 ( 2160)
  Misc. bond           : bond        0.00048 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6919 (t80)
REVERT: A   53 ASP cc_start: 0.7979 (m-30) cc_final: 0.7775 (m-30)
REVERT: B   34 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7064 (t80)
REVERT: B  100 LEU cc_start: 0.9066 (tp) cc_final: 0.8778 (mt)
REVERT: B  125 PHE cc_start: 0.8512 (t80) cc_final: 0.8291 (t80)
REVERT: B  191 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (ttm)
REVERT: B  205 TYR cc_start: 0.8168 (t80) cc_final: 0.7900 (t80)
REVERT: C   80 MET cc_start: 0.6814 (mtm) cc_final: 0.6459 (mtm)
REVERT: C  147 MET cc_start: 0.7143 (ttt) cc_final: 0.6750 (ttm)
REVERT: C  163 MET cc_start: 0.8295 (mtp) cc_final: 0.7847 (mtp)
REVERT: C  177 ASN cc_start: 0.8174 (m-40) cc_final: 0.7693 (m-40)
REVERT: C  191 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8226 (ttm)
REVERT: C  192 TYR cc_start: 0.8349 (m-80) cc_final: 0.8038 (m-80)
REVERT: C  206 PHE cc_start: 0.8399 (t80) cc_final: 0.8165 (t80)
REVERT: D  171 GLU cc_start: 0.7878 (tt0) cc_final: 0.7549 (tt0)
REVERT: D  192 TYR cc_start: 0.8102 (m-80) cc_final: 0.7848 (m-80)
REVERT: D  205 TYR cc_start: 0.8075 (t80) cc_final: 0.7674 (t80)
REVERT: E   35 TRP cc_start: 0.8001 (m100) cc_final: 0.7688 (m100)
REVERT: E   80 MET cc_start: 0.6527 (mtm) cc_final: 0.6253 (mtp)
REVERT: E  138 PHE cc_start: 0.8391 (m-80) cc_final: 0.8148 (m-80)
REVERT: E  141 MET cc_start: 0.8270 (mtp) cc_final: 0.8029 (ttm)
REVERT: E  191 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8280 (ttm)
  outliers start: 31
  outliers final: 19
  residues processed: 212
  average time/residue: 0.2848
  time to fit residues: 67.8519
Evaluate side-chains
  212 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  138 PHE
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  177 ASN
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 94 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 241 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.161521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.137059 restraints weight = 9271.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.18
r_work: 0.3262 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8935  Z= 0.145
  Angle     :  0.498   6.843  12195  Z= 0.260
  Chirality :  0.037   0.112   1370
  Planarity :  0.003   0.029   1450
  Dihedral  :  9.751 111.451   1215
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 12.77 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.25), residues: 1065
  helix:  1.91 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.47 (0.53), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  52 
 TYR   0.013   0.001   TYR C 187 
 PHE   0.010   0.001   PHE A 138 
 TRP   0.010   0.001   TRP D  75 
 HIS   0.003   0.001   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8930)
  covalent geometry    : angle       0.49794 (12195)
  hydrogen bonds       : bond        0.04771 (  720)
  hydrogen bonds       : angle       3.62629 ( 2160)
  Misc. bond           : bond        0.00051 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7052 (t80)
REVERT: B   34 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7142 (t80)
REVERT: B  100 LEU cc_start: 0.9069 (tp) cc_final: 0.8779 (mt)
REVERT: B  191 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8501 (ttm)
REVERT: B  205 TYR cc_start: 0.8171 (t80) cc_final: 0.7890 (t80)
REVERT: C   80 MET cc_start: 0.6860 (mtm) cc_final: 0.6485 (mtm)
REVERT: C  147 MET cc_start: 0.7150 (ttt) cc_final: 0.6759 (ttm)
REVERT: C  163 MET cc_start: 0.8316 (mtp) cc_final: 0.7851 (mtp)
REVERT: C  177 ASN cc_start: 0.8161 (m-40) cc_final: 0.7657 (m-40)
REVERT: C  191 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8087 (ttm)
REVERT: C  192 TYR cc_start: 0.8388 (m-80) cc_final: 0.8117 (m-80)
REVERT: C  206 PHE cc_start: 0.8396 (t80) cc_final: 0.8169 (t80)
REVERT: D  171 GLU cc_start: 0.7904 (tt0) cc_final: 0.7545 (tt0)
REVERT: D  192 TYR cc_start: 0.8166 (m-80) cc_final: 0.7922 (m-80)
REVERT: D  205 TYR cc_start: 0.8072 (t80) cc_final: 0.7712 (t80)
REVERT: E   34 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6949 (t80)
REVERT: E   35 TRP cc_start: 0.7993 (m100) cc_final: 0.7711 (m100)
REVERT: E   80 MET cc_start: 0.6503 (mtm) cc_final: 0.6247 (mtp)
REVERT: E  141 MET cc_start: 0.8195 (mtp) cc_final: 0.7956 (ttm)
REVERT: E  191 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8102 (ttm)
REVERT: E  205 TYR cc_start: 0.8245 (t80) cc_final: 0.8045 (t80)
  outliers start: 33
  outliers final: 19
  residues processed: 216
  average time/residue: 0.2849
  time to fit residues: 69.0897
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  138 PHE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 35 optimal weight:   30.0000
   chunk 68 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 78 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.162631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.138355 restraints weight = 9210.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.17
r_work: 0.3251 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8935  Z= 0.152
  Angle     :  0.504   6.827  12195  Z= 0.265
  Chirality :  0.037   0.116   1370
  Planarity :  0.004   0.030   1450
  Dihedral  :  9.604 110.853   1215
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 13.90 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.25), residues: 1065
  helix:  1.91 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.42 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  52 
 TYR   0.014   0.001   TYR A 187 
 PHE   0.027   0.002   PHE B 125 
 TRP   0.010   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8930)
  covalent geometry    : angle       0.50440 (12195)
  hydrogen bonds       : bond        0.04854 (  720)
  hydrogen bonds       : angle       3.62585 ( 2160)
  Misc. bond           : bond        0.00056 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7013 (t80)
REVERT: B   34 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7112 (t80)
REVERT: B  100 LEU cc_start: 0.9052 (tp) cc_final: 0.8785 (mt)
REVERT: B  191 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (ttm)
REVERT: B  203 VAL cc_start: 0.8114 (t) cc_final: 0.7900 (t)
REVERT: C   80 MET cc_start: 0.6890 (mtm) cc_final: 0.6539 (mtm)
REVERT: C  147 MET cc_start: 0.7014 (ttt) cc_final: 0.6705 (ttm)
REVERT: C  163 MET cc_start: 0.8312 (mtp) cc_final: 0.7846 (mtp)
REVERT: C  177 ASN cc_start: 0.8145 (m-40) cc_final: 0.7669 (m-40)
REVERT: C  191 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8100 (ttm)
REVERT: C  192 TYR cc_start: 0.8387 (m-80) cc_final: 0.8130 (m-80)
REVERT: C  206 PHE cc_start: 0.8380 (t80) cc_final: 0.8150 (t80)
REVERT: D  171 GLU cc_start: 0.7889 (tt0) cc_final: 0.7531 (tt0)
REVERT: D  192 TYR cc_start: 0.8105 (m-80) cc_final: 0.7905 (m-80)
REVERT: D  205 TYR cc_start: 0.8055 (t80) cc_final: 0.7754 (t80)
REVERT: E   34 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6933 (t80)
REVERT: E   35 TRP cc_start: 0.8003 (m100) cc_final: 0.7709 (m100)
REVERT: E  141 MET cc_start: 0.8154 (mtp) cc_final: 0.7926 (ttm)
REVERT: E  185 SER cc_start: 0.8561 (m) cc_final: 0.8351 (m)
REVERT: E  191 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8045 (ttm)
REVERT: E  205 TYR cc_start: 0.8224 (t80) cc_final: 0.7910 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 204
  average time/residue: 0.2917
  time to fit residues: 66.5588
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  138 PHE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  177 ASN
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 27 optimal weight:   50.0000
   chunk 90 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 97 optimal weight:    1.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.160663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.136469 restraints weight = 9201.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.16
r_work: 0.3243 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8935  Z= 0.174
  Angle     :  0.530   7.057  12195  Z= 0.277
  Chirality :  0.038   0.117   1370
  Planarity :  0.004   0.031   1450
  Dihedral  :  9.554 110.828   1215
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 13.79 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.25), residues: 1065
  helix:  1.86 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.45 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  52 
 TYR   0.016   0.001   TYR A 187 
 PHE   0.021   0.002   PHE B 125 
 TRP   0.010   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8930)
  covalent geometry    : angle       0.52983 (12195)
  hydrogen bonds       : bond        0.05083 (  720)
  hydrogen bonds       : angle       3.66612 ( 2160)
  Misc. bond           : bond        0.00070 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 193
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6904 (t80)
REVERT: B   34 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7083 (t80)
REVERT: B  100 LEU cc_start: 0.9087 (tp) cc_final: 0.8812 (mt)
REVERT: B  191 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8503 (ttm)
REVERT: B  203 VAL cc_start: 0.8174 (t) cc_final: 0.7955 (t)
REVERT: C   80 MET cc_start: 0.6892 (mtm) cc_final: 0.6554 (mtm)
REVERT: C  147 MET cc_start: 0.7101 (ttt) cc_final: 0.6698 (ttm)
REVERT: C  163 MET cc_start: 0.8539 (mtp) cc_final: 0.8132 (mtp)
REVERT: C  177 ASN cc_start: 0.8175 (m-40) cc_final: 0.7669 (m-40)
REVERT: C  191 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8083 (ttm)
REVERT: C  192 TYR cc_start: 0.8339 (m-80) cc_final: 0.8108 (m-80)
REVERT: C  206 PHE cc_start: 0.8390 (t80) cc_final: 0.8155 (t80)
REVERT: D  171 GLU cc_start: 0.7936 (tt0) cc_final: 0.7553 (tt0)
REVERT: D  192 TYR cc_start: 0.8190 (m-80) cc_final: 0.7988 (m-80)
REVERT: D  205 TYR cc_start: 0.8064 (t80) cc_final: 0.7795 (t80)
REVERT: E   34 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6935 (t80)
REVERT: E   35 TRP cc_start: 0.8082 (m100) cc_final: 0.7743 (m100)
REVERT: E  141 MET cc_start: 0.8119 (mtp) cc_final: 0.7872 (ttm)
REVERT: E  185 SER cc_start: 0.8577 (m) cc_final: 0.8367 (m)
REVERT: E  191 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8301 (ttm)
REVERT: E  205 TYR cc_start: 0.8219 (t80) cc_final: 0.8018 (t80)
  outliers start: 35
  outliers final: 22
  residues processed: 212
  average time/residue: 0.2864
  time to fit residues: 68.2337
Evaluate side-chains
  213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  177 ASN
Chi-restraints excluded: chain D residue  203 VAL
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 63 optimal weight:   50.0000
   chunk 30 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 21 optimal weight:   50.0000
   chunk 98 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 96 optimal weight:   20.0000
   chunk 74 optimal weight:    7.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.160909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.136762 restraints weight = 9241.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.17
r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8935  Z= 0.192
  Angle     :  0.557   8.637  12195  Z= 0.290
  Chirality :  0.039   0.122   1370
  Planarity :  0.004   0.031   1450
  Dihedral  :  9.417 110.366   1215
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.14 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.25), residues: 1065
  helix:  1.77 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.49 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  52 
 TYR   0.017   0.001   TYR A 187 
 PHE   0.020   0.002   PHE D 125 
 TRP   0.010   0.002   TRP D  84 
 HIS   0.003   0.002   HIS E  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 8930)
  covalent geometry    : angle       0.55678 (12195)
  hydrogen bonds       : bond        0.05300 (  720)
  hydrogen bonds       : angle       3.75896 ( 2160)
  Misc. bond           : bond        0.00078 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 189
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.6783 (t80)
REVERT: B   34 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7108 (t80)
REVERT: B  100 LEU cc_start: 0.9114 (tp) cc_final: 0.8841 (mt)
REVERT: B  191 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8666 (ttm)
REVERT: B  203 VAL cc_start: 0.8202 (t) cc_final: 0.7975 (t)
REVERT: C   80 MET cc_start: 0.6908 (mtm) cc_final: 0.6568 (mtm)
REVERT: C  147 MET cc_start: 0.7081 (ttt) cc_final: 0.6716 (ttm)
REVERT: C  163 MET cc_start: 0.8546 (mtp) cc_final: 0.8108 (mtp)
REVERT: C  177 ASN cc_start: 0.8147 (m-40) cc_final: 0.7613 (m-40)
REVERT: C  191 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8361 (ttm)
REVERT: C  192 TYR cc_start: 0.8442 (m-80) cc_final: 0.8218 (m-80)
REVERT: C  206 PHE cc_start: 0.8281 (t80) cc_final: 0.8038 (t80)
REVERT: D  171 GLU cc_start: 0.7919 (tt0) cc_final: 0.7562 (tt0)
REVERT: D  205 TYR cc_start: 0.8034 (t80) cc_final: 0.7817 (t80)
REVERT: E   34 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.6947 (t80)
REVERT: E   35 TRP cc_start: 0.8058 (m100) cc_final: 0.7713 (m100)
REVERT: E  141 MET cc_start: 0.8166 (mtp) cc_final: 0.7957 (ttm)
REVERT: E  185 SER cc_start: 0.8591 (m) cc_final: 0.8378 (m)
REVERT: E  191 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8326 (ttm)
  outliers start: 31
  outliers final: 20
  residues processed: 205
  average time/residue: 0.2921
  time to fit residues: 66.9177
Evaluate side-chains
  204 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  203 VAL
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 75 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.162611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.138726 restraints weight = 9193.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.15
r_work: 0.3262 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8935  Z= 0.133
  Angle     :  0.497   9.247  12195  Z= 0.260
  Chirality :  0.036   0.123   1370
  Planarity :  0.003   0.029   1450
  Dihedral  :  9.203 112.082   1215
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.93 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.25), residues: 1065
  helix:  1.96 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.36 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  52 
 TYR   0.015   0.001   TYR C 187 
 PHE   0.018   0.001   PHE B 125 
 TRP   0.009   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8930)
  covalent geometry    : angle       0.49731 (12195)
  hydrogen bonds       : bond        0.04614 (  720)
  hydrogen bonds       : angle       3.60708 ( 2160)
  Misc. bond           : bond        0.00048 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 186
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6986 (t80)
REVERT: B   29 TYR cc_start: 0.7220 (m-10) cc_final: 0.7012 (m-10)
REVERT: B   34 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7143 (t80)
REVERT: B  100 LEU cc_start: 0.9070 (tp) cc_final: 0.8771 (mt)
REVERT: B  132 SER cc_start: 0.8418 (p) cc_final: 0.8048 (p)
REVERT: B  191 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8465 (ttm)
REVERT: C   80 MET cc_start: 0.6907 (mtm) cc_final: 0.6652 (mtm)
REVERT: C  147 MET cc_start: 0.6976 (ttt) cc_final: 0.6706 (ttm)
REVERT: C  163 MET cc_start: 0.8292 (mtp) cc_final: 0.7931 (mtp)
REVERT: C  177 ASN cc_start: 0.8151 (m-40) cc_final: 0.7628 (m-40)
REVERT: C  191 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8102 (ttm)
REVERT: C  206 PHE cc_start: 0.8240 (t80) cc_final: 0.7980 (t80)
REVERT: D  171 GLU cc_start: 0.7913 (tt0) cc_final: 0.7561 (tt0)
REVERT: D  205 TYR cc_start: 0.7995 (t80) cc_final: 0.7787 (t80)
REVERT: E   34 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: E  141 MET cc_start: 0.8172 (mtp) cc_final: 0.7903 (ttm)
REVERT: E  185 SER cc_start: 0.8540 (m) cc_final: 0.8332 (m)
REVERT: E  191 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7988 (ttm)
  outliers start: 31
  outliers final: 18
  residues processed: 202
  average time/residue: 0.2914
  time to fit residues: 65.7869
Evaluate side-chains
  207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  203 VAL
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:   20.0000
   overall best weight:    6.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.159807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.135907 restraints weight = 9269.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.16
r_work: 0.3234 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8935  Z= 0.191
  Angle     :  0.562  10.881  12195  Z= 0.295
  Chirality :  0.040   0.181   1370
  Planarity :  0.004   0.031   1450
  Dihedral  :  8.545 109.348   1215
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.16 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.25), residues: 1065
  helix:  1.80 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.40 (0.56), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  52 
 TYR   0.017   0.002   TYR A 187 
 PHE   0.020   0.002   PHE D 125 
 TRP   0.010   0.002   TRP D  84 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8930)
  covalent geometry    : angle       0.56233 (12195)
  hydrogen bonds       : bond        0.05219 (  720)
  hydrogen bonds       : angle       3.76260 ( 2160)
  Misc. bond           : bond        0.00074 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6790 (t80)
REVERT: B   34 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7080 (t80)
REVERT: B  100 LEU cc_start: 0.9072 (tp) cc_final: 0.8765 (mt)
REVERT: B  184 GLN cc_start: 0.8701 (mt0) cc_final: 0.8455 (mt0)
REVERT: B  191 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (ttm)
REVERT: C   80 MET cc_start: 0.6869 (mtm) cc_final: 0.6579 (mtm)
REVERT: C  147 MET cc_start: 0.6975 (ttt) cc_final: 0.6666 (ttm)
REVERT: C  163 MET cc_start: 0.8524 (mtp) cc_final: 0.8097 (mtp)
REVERT: C  191 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8278 (ttm)
REVERT: C  206 PHE cc_start: 0.8387 (t80) cc_final: 0.8159 (t80)
REVERT: D  171 GLU cc_start: 0.7936 (tt0) cc_final: 0.7574 (tt0)
REVERT: D  187 TYR cc_start: 0.8456 (t80) cc_final: 0.8194 (t80)
REVERT: E   34 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6927 (t80)
REVERT: E   35 TRP cc_start: 0.8062 (m100) cc_final: 0.7737 (m100)
REVERT: E  141 MET cc_start: 0.8121 (mtp) cc_final: 0.7892 (ttm)
REVERT: E  185 SER cc_start: 0.8584 (m) cc_final: 0.8368 (m)
REVERT: E  191 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8227 (ttm)
  outliers start: 30
  outliers final: 19
  residues processed: 202
  average time/residue: 0.2970
  time to fit residues: 66.9618
Evaluate side-chains
  208 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  158 LEU
Chi-restraints excluded: chain D residue  203 VAL
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 100 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0060
   chunk 95 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   overall best weight:    3.8004

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.161914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.138078 restraints weight = 9308.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.16
r_work: 0.3261 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8935  Z= 0.144
  Angle     :  0.513  11.853  12195  Z= 0.271
  Chirality :  0.038   0.191   1370
  Planarity :  0.004   0.030   1450
  Dihedral  :  8.594 110.917   1215
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.29 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.36 (0.25), residues: 1065
  helix:  1.92 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.30 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  52 
 TYR   0.015   0.001   TYR C 111 
 PHE   0.020   0.002   PHE E 206 
 TRP   0.009   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8930)
  covalent geometry    : angle       0.51279 (12195)
  hydrogen bonds       : bond        0.04713 (  720)
  hydrogen bonds       : angle       3.65422 ( 2160)
  Misc. bond           : bond        0.00058 (    5)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 184
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6885 (t80)
REVERT: B   34 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7094 (t80)
REVERT: B  100 LEU cc_start: 0.9062 (tp) cc_final: 0.8725 (mt)
REVERT: B  132 SER cc_start: 0.8366 (p) cc_final: 0.8003 (p)
REVERT: B  184 GLN cc_start: 0.8671 (mt0) cc_final: 0.8424 (mt0)
REVERT: B  191 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8474 (ttm)
REVERT: B  203 VAL cc_start: 0.8120 (t) cc_final: 0.7904 (t)
REVERT: C   80 MET cc_start: 0.6855 (mtm) cc_final: 0.6586 (mtm)
REVERT: C  147 MET cc_start: 0.6959 (ttt) cc_final: 0.6670 (ttm)
REVERT: C  163 MET cc_start: 0.8286 (mtp) cc_final: 0.7890 (mtp)
REVERT: C  191 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8069 (ttm)
REVERT: C  206 PHE cc_start: 0.8231 (t80) cc_final: 0.7966 (t80)
REVERT: D  171 GLU cc_start: 0.7876 (tt0) cc_final: 0.7515 (tt0)
REVERT: E   34 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6936 (t80)
REVERT: E  141 MET cc_start: 0.8076 (mtp) cc_final: 0.7810 (ttm)
REVERT: E  185 SER cc_start: 0.8540 (m) cc_final: 0.8326 (m)
REVERT: E  191 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7959 (ttm)
  outliers start: 23
  outliers final: 16
  residues processed: 194
  average time/residue: 0.2991
  time to fit residues: 64.5911
Evaluate side-chains
  199 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain B residue   34 PHE
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  177 ASN
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  138 PHE
Chi-restraints excluded: chain D residue  203 VAL
Chi-restraints excluded: chain E residue   34 PHE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue  191 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:   50.0000
   chunk 63 optimal weight:   50.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.160904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.137077 restraints weight = 9218.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.16
r_work: 0.3244 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8935  Z= 0.165
  Angle     :  0.532   8.867  12195  Z= 0.282
  Chirality :  0.039   0.230   1370
  Planarity :  0.004   0.030   1450
  Dihedral  :  8.551 109.858   1215
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.06 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.25), residues: 1065
  helix:  1.85 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.33 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  52 
 TYR   0.017   0.001   TYR A 187 
 PHE   0.023   0.002   PHE D 125 
 TRP   0.010   0.001   TRP D  75 
 HIS   0.003   0.002   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8930)
  covalent geometry    : angle       0.53194 (12195)
  hydrogen bonds       : bond        0.04959 (  720)
  hydrogen bonds       : angle       3.69484 ( 2160)
  Misc. bond           : bond        0.00065 (    5)

===============================================================================
Job complete
usr+sys time: 2480.79 seconds
wall clock time: 42 minutes 59.24 seconds (2579.24 seconds total)