Starting phenix.real_space_refine
on Thu Jun  4 06:28:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w20_65561/06_2026/9w20_65561.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      80      5.16       5
     C    6828      2.51       5
     N    1872      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10806
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2697
          Classifications: {'peptide': 338}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "a"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2706
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 322}
    Chain: "B"
      Number of atoms: 2697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2697
          Classifications: {'peptide': 338}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "b"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2706
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 322}
  Time building chain proxies: 2.56, per 1000 atoms: 0.24
  Number of scatterers: 10806
  At special positions: 0
  Unit cell: (96.624, 122.122, 92.598, 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      80     16.00
     O    2026      8.00
     N    1872      7.00
     C    6828      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  55 " - pdb=" SG  CYS a 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 179 " - pdb=" SG  CYS a 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 280 " - pdb=" SG  CYS a 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 291 " - pdb=" SG  CYS a 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 313 " - pdb=" SG  CYS a 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  55 " - pdb=" SG  CYS b 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 179 " - pdb=" SG  CYS b 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 280 " - pdb=" SG  CYS b 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 291 " - pdb=" SG  CYS b 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 313 " - pdb=" SG  CYS b 316 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 535.2 milliseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2516

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      17.4% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 51
      removed outlier: 3.794A  pdb=" N   GLU A  51 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 82
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.632A  pdb=" N   MET A 241 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'a' and resid 38 through 51
    Processing helix  chain 'a' and resid 61 through 81
      Proline residue:  a  73  - end of helix
    Processing helix  chain 'a' and resid 117 through 121
      removed outlier: 3.893A  pdb=" N   ALA a 121 " --> pdb=" O   TRP a 118 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 144 through 148
    Processing helix  chain 'a' and resid 226 through 230
      removed outlier: 3.607A  pdb=" N   HIS a 229 " --> pdb=" O   PRO a 226 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 244 through 248
      removed outlier: 3.595A  pdb=" N   ALA a 248 " --> pdb=" O   LYS a 245 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 267 through 271
      removed outlier: 3.947A  pdb=" N   LEU a 270 " --> pdb=" O   PRO a 267 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY a 271 " --> pdb=" O   TRP a 268 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 267 through 271'
    Processing helix  chain 'B' and resid 41 through 51
      removed outlier: 4.060A  pdb=" N   GLU B  51 " --> pdb=" O   GLN B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 82
      Proline residue:  B  73  - end of helix
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.531A  pdb=" N   GLY B 119 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.580A  pdb=" N   HIS B 229 " --> pdb=" O   PRO B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'b' and resid 38 through 53
      removed outlier: 3.725A  pdb=" N   LEU b  42 " --> pdb=" O   SER b  38 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 61 through 82
      Proline residue:  b  73  - end of helix
    Processing helix  chain 'b' and resid 114 through 120
      removed outlier: 4.226A  pdb=" N   TRP b 118 " --> pdb=" O   SER b 114 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 144 through 148
    Processing helix  chain 'b' and resid 226 through 230
    Processing helix  chain 'b' and resid 237 through 241
      removed outlier: 3.981A  pdb=" N   MET b 241 " --> pdb=" O   GLU b 238 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 244 through 248
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 157
      removed outlier: 6.995A  pdb=" N   TRP A 168 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 217
      removed outlier: 5.459A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 186 " --> pdb=" O   ILE a 188 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   ALA a 205 " --> pdb=" O   ILE a 212 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   ILE a 212 " --> pdb=" O   ALA a 205 " (cutoff:3.500A)
      removed outlier: 8.704A  pdb=" N   GLU a 213 " --> pdb=" O   PHE a 277 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE a 277 " --> pdb=" O   GLU a 213 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASP a 276 " --> pdb=" O   ARG a 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276
      removed outlier: 3.864A  pdb=" N   LEU A 298 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'a' and resid 32 through 36
      removed outlier: 6.290A  pdb=" N   LYS a  33 " --> pdb=" O   ILE a 167 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   LEU a 169 " --> pdb=" O   LYS a  33 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLN a  35 " --> pdb=" O   LEU a 169 " (cutoff:3.500A)
      removed outlier: 8.544A  pdb=" N   LEU a 171 " --> pdb=" O   GLN a  35 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'a' and resid 285 through 287
      removed outlier: 6.568A  pdb=" N   VAL a 286 " --> pdb=" O   CYS a 313 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57
      removed outlier: 3.583A  pdb=" N   MET B  89 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE B 135 " --> pdb=" O   MET B  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 155
    Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 331
      removed outlier: 3.630A  pdb=" N   TYR B 323 " --> pdb=" O   TRP B 330 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP B 276 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE B 277 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   GLU B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS B 189 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ALA b 205 " --> pdb=" O   ILE b 212 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE b 212 " --> pdb=" O   ALA b 205 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   GLU b 213 " --> pdb=" O   PHE b 277 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE b 277 " --> pdb=" O   GLU b 213 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ARG b 324 " --> pdb=" O   GLU b 274 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU b 298 " --> pdb=" O   TYR b 331 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287
      removed outlier: 6.207A  pdb=" N   THR B 284 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   CYS B 313 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'b' and resid 57 through 58
    Processing sheet with id=AB3, first strand: chain 'b' and resid 88 through 90
    Processing sheet with id=AB4, first strand: chain 'b' and resid 153 through 154
    Processing sheet with id=AB5, first strand: chain 'b' and resid 286 through 287
      removed outlier: 7.092A  pdb=" N   VAL b 286 " --> pdb=" O   CYS b 313 " (cutoff:3.500A)

    231 hydrogen bonds defined for protein.
    582 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: 1.23

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3516
        1.34 -     1.46: 2665
        1.46 -     1.58: 4789
        1.58 -     1.70: 0
        1.70 -     1.82: 116
  Bond restraints: 11086
  Sorted by residual:
  bond pdb=" CG  ARG A 174 "
       pdb=" CD  ARG A 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.12e+00
  bond pdb=" CG  ARG b 174 "
       pdb=" CD  ARG b 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.29e-01
  bond pdb=" CA  ILE B 167 "
       pdb=" CB  ILE B 167 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.31e-02 5.83e+03 8.54e-01
  bond pdb=" CG  MET b 198 "
       pdb=" SD  MET b 198 "
    ideal  model  delta    sigma   weight residual
    1.803  1.825 -0.022 2.50e-02 1.60e+03 7.46e-01
  bond pdb=" CB  ARG A 174 "
       pdb=" CG  ARG A 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.69e-01
  ... (remaining 11081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 14913
        2.37 -     4.74: 106
        4.74 -     7.11: 12
        7.11 -     9.48: 2
        9.48 -    11.85: 1
  Bond angle restraints: 15034
  Sorted by residual:
  angle pdb=" C   ASP a 136 "
        pdb=" CA  ASP a 136 "
        pdb=" CB  ASP a 136 "
      ideal   model   delta    sigma   weight residual
     115.89  110.55    5.34 1.32e+00 5.74e-01 1.64e+01
  angle pdb=" CB  MET b 198 "
        pdb=" CG  MET b 198 "
        pdb=" SD  MET b 198 "
      ideal   model   delta    sigma   weight residual
     112.70  124.55  -11.85 3.00e+00 1.11e-01 1.56e+01
  angle pdb=" CG  ARG A 174 "
        pdb=" CD  ARG A 174 "
        pdb=" NE  ARG A 174 "
      ideal   model   delta    sigma   weight residual
     112.00  117.75   -5.75 2.20e+00 2.07e-01 6.82e+00
  angle pdb=" CG  MET b 198 "
        pdb=" SD  MET b 198 "
        pdb=" CE  MET b 198 "
      ideal   model   delta    sigma   weight residual
     100.90  106.56   -5.66 2.20e+00 2.07e-01 6.63e+00
  angle pdb=" CB  MET b  89 "
        pdb=" CG  MET b  89 "
        pdb=" SD  MET b  89 "
      ideal   model   delta    sigma   weight residual
     112.70  120.35   -7.65 3.00e+00 1.11e-01 6.50e+00
  ... (remaining 15029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 5578
       17.63 -    35.27: 778
       35.27 -    52.90: 229
       52.90 -    70.53: 42
       70.53 -    88.17: 19
  Dihedral angle restraints: 6646
    sinusoidal: 2748
      harmonic: 3898
  Sorted by residual:
  dihedral pdb=" CB  CYS B  55 "
           pdb=" SG  CYS B  55 "
           pdb=" SG  CYS B 143 "
           pdb=" CB  CYS B 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.66   79.66     1      1.00e+01 1.00e-02 7.88e+01
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 316 "
           pdb=" CB  CYS B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.27   78.27     1      1.00e+01 1.00e-02 7.65e+01
  dihedral pdb=" CB  CYS B 291 "
           pdb=" SG  CYS B 291 "
           pdb=" SG  CYS B 312 "
           pdb=" CB  CYS B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.37   75.37     1      1.00e+01 1.00e-02 7.18e+01
  ... (remaining 6643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1007
       0.027 -    0.054: 395
       0.054 -    0.081: 96
       0.081 -    0.108: 93
       0.108 -    0.135: 27
  Chirality restraints: 1618
  Sorted by residual:
  chirality pdb=" CA  ILE b  57 "
            pdb=" N   ILE b  57 "
            pdb=" C   ILE b  57 "
            pdb=" CB  ILE b  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE B  57 "
            pdb=" N   ILE B  57 "
            pdb=" C   ILE B  57 "
            pdb=" CB  ILE B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CB  ILE a  57 "
            pdb=" CA  ILE a  57 "
            pdb=" CG1 ILE a  57 "
            pdb=" CG2 ILE a  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1615 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  41 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   LYS B  41 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS B  41 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B  42 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 118 "   -0.013 2.00e-02 2.50e+03   9.58e-03 2.30e+00
        pdb=" CG  TRP B 118 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 118 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 118 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 118 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 118 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 118 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 118 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 118 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  71 "   -0.006 2.00e-02 2.50e+03   1.17e-02 1.36e+00
        pdb=" C   ILE B  71 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ILE B  71 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   THR B  72 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 326
        2.68 -     3.24: 9965
        3.24 -     3.79: 15611
        3.79 -     4.35: 19518
        4.35 -     4.90: 33161
  Nonbonded interactions: 78581
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP b 136 "
            pdb=" N   GLY b 137 "
     model   vdw
     2.126 3.120
  nonbonded pdb=" OG  SER a 103 "
            pdb=" OG  SER a 152 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" O   SER A 233 "
            pdb=" OG  SER A 233 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   SER B 233 "
            pdb=" OG  SER B 233 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   SER b 233 "
            pdb=" OG  SER b 233 "
     model   vdw
     2.205 3.040
  ... (remaining 78576 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = (chain 'a' and resid 15 through 352)
  selection = (chain 'b' and resid 15 through 352)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.140
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
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      :  0.003   0.032  11106  Z= 0.115
  Angle     :  0.507  11.855  15074  Z= 0.263
  Chirality :  0.038   0.135   1618
  Planarity :  0.003   0.029   1914
  Dihedral  : 17.784  88.165   4070
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 29.17 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.57 (0.23), residues: 1346
  helix:  2.25 (0.46), residues: 148
  sheet: -1.54 (0.38), residues: 214
  loop : -1.55 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 174 
 TYR   0.009   0.001   TYR a 158 
 PHE   0.007   0.001   PHE a 217 
 TRP   0.025   0.001   TRP B 118 
 HIS   0.005   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 (11086)
  covalent geometry    : angle       0.50657 /  0.26 (15034)
  SS BOND              : bond        0.00196 /  0.13 (   20)
  SS BOND              : angle       0.64274 /  0.42 (   40)
  hydrogen bonds       : bond        0.23638 / 15.20 (  231)
  hydrogen bonds       : angle       7.89402 /  5.78 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7430 (p-80)
REVERT: A   67 MET cc_start: 0.8800 (ttp) cc_final: 0.7646 (tmm)
REVERT: A  160 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5663 (t80)
REVERT: a   37 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7924 (tt0)
REVERT: a   67 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8118 (tmm)
REVERT: a   71 ILE cc_start: 0.7698 (tt) cc_final: 0.7408 (tt)
REVERT: a   89 MET cc_start: 0.7762 (mpp) cc_final: 0.7358 (mpp)
REVERT: a  154 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: a  331 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8192 (m-10)
REVERT: a  333 MET cc_start: 0.7767 (mtp) cc_final: 0.7531 (mtp)
REVERT: a  341 LYS cc_start: 0.8431 (pttm) cc_final: 0.8201 (pttm)
REVERT: B   67 MET cc_start: 0.8639 (tmm) cc_final: 0.8239 (tmm)
REVERT: B  156 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: B  234 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8961 (p0)
REVERT: B  333 MET cc_start: 0.7887 (mtp) cc_final: 0.7560 (mtp)
REVERT: b   67 MET cc_start: 0.8862 (tmm) cc_final: 0.8230 (tmm)
REVERT: b  139 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7707 (tm-30)
REVERT: b  160 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6653 (t80)
  outliers start: 57
  outliers final: 44
  residues processed: 153
  average time/residue: 0.0854
  time to fit residues: 19.9735
Evaluate side-chains
  159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 106
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue   37 GLU
Chi-restraints excluded: chain a residue   42 LEU
Chi-restraints excluded: chain a residue   61 THR
Chi-restraints excluded: chain a residue   67 MET
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  177 VAL
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   38 SER
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  139 GLU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  163 PHE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  204 SER
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  318 LEU
Chi-restraints excluded: chain b residue  329 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.1980
   chunk 77 optimal weight:    0.0980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  26 HIS
** a 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 GLN
B 263 GLN
b 107 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.153924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.095884 restraints weight = 15340.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.100279 restraints weight = 8159.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.103044 restraints weight = 5764.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.104744 restraints weight = 4733.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105630 restraints weight = 4229.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  11106  Z= 0.092
  Angle     :  0.492   6.717  15074  Z= 0.256
  Chirality :  0.039   0.151   1618
  Planarity :  0.003   0.022   1914
  Dihedral  :  7.126  57.914   1527
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 27.40 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.61 (0.22), residues: 1346
  helix:  2.11 (0.46), residues: 148
  sheet: -1.65 (0.36), residues: 225
  loop : -1.53 (0.19), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.014   0.001   TYR B 323 
 PHE   0.007   0.001   PHE A 217 
 TRP   0.013   0.001   TRP B 118 
 HIS   0.003   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.09 (11086)
  covalent geometry    : angle       0.49061 /  0.26 (15034)
  SS BOND              : bond        0.00243 /  0.16 (   20)
  SS BOND              : angle       0.76352 /  0.45 (   40)
  hydrogen bonds       : bond        0.04055 /  2.56 (  231)
  hydrogen bonds       : angle       5.54355 /  3.98 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 115
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8487 (ttp) cc_final: 0.7263 (tmm)
REVERT: A  160 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5356 (t80)
REVERT: A  275 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8062 (ttm)
REVERT: A  312 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6523 (t)
REVERT: A  322 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.6954 (ptm160)
REVERT: a   67 MET cc_start: 0.8647 (tmm) cc_final: 0.7917 (tmm)
REVERT: a   71 ILE cc_start: 0.7145 (tt) cc_final: 0.6605 (tt)
REVERT: a   89 MET cc_start: 0.7554 (mpp) cc_final: 0.7078 (mpp)
REVERT: a  171 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8613 (tt)
REVERT: a  206 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8624 (tp)
REVERT: a  234 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8794 (p0)
REVERT: a  275 MET cc_start: 0.8110 (mmm) cc_final: 0.7902 (ttm)
REVERT: a  331 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.7890 (m-10)
REVERT: a  333 MET cc_start: 0.7733 (mtp) cc_final: 0.7457 (mtp)
REVERT: a  341 LYS cc_start: 0.8267 (pttm) cc_final: 0.8001 (pttm)
REVERT: B   67 MET cc_start: 0.8512 (tmm) cc_final: 0.8096 (tmm)
REVERT: B   86 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: B  156 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: B  333 MET cc_start: 0.8008 (mtp) cc_final: 0.7575 (mtp)
REVERT: b   67 MET cc_start: 0.8555 (tmm) cc_final: 0.7991 (tmm)
REVERT: b  160 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6069 (t80)
  outliers start: 57
  outliers final: 27
  residues processed: 162
  average time/residue: 0.0865
  time to fit residues: 21.1289
Evaluate side-chains
  146 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  312 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  171 LEU
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  241 MET
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  163 PHE
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Chi-restraints excluded: chain b residue  348 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 119 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 22 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 127 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
a 263 GLN
** a 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.148525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.090342 restraints weight = 15860.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.094333 restraints weight = 8699.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.096858 restraints weight = 6267.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.098434 restraints weight = 5202.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.099372 restraints weight = 4653.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11106  Z= 0.222
  Angle     :  0.566   6.934  15074  Z= 0.297
  Chirality :  0.041   0.171   1618
  Planarity :  0.003   0.030   1914
  Dihedral  :  6.669  56.839   1475
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 26.56 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.87 (0.22), residues: 1346
  helix:  1.73 (0.45), residues: 148
  sheet: -1.61 (0.35), residues: 235
  loop : -1.74 (0.18), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 192 
 TYR   0.012   0.001   TYR A 113 
 PHE   0.015   0.001   PHE b 217 
 TRP   0.013   0.002   TRP a 225 
 HIS   0.007   0.001   HIS B 129 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00521 /  0.22 (11086)
  covalent geometry    : angle       0.56491 /  0.30 (15034)
  SS BOND              : bond        0.00370 /  0.24 (   20)
  SS BOND              : angle       0.89275 /  0.55 (   40)
  hydrogen bonds       : bond        0.04603 /  2.87 (  231)
  hydrogen bonds       : angle       5.63226 /  4.01 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 108
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8772 (ttp) cc_final: 0.7541 (tmm)
REVERT: A  160 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5327 (t80)
REVERT: A  240 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8251 (mm-30)
REVERT: a   67 MET cc_start: 0.8770 (tmm) cc_final: 0.7924 (tmm)
REVERT: a   71 ILE cc_start: 0.7093 (tt) cc_final: 0.6623 (tt)
REVERT: a   89 MET cc_start: 0.7421 (mpp) cc_final: 0.6953 (mpp)
REVERT: a  154 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6514 (mp0)
REVERT: a  206 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8693 (tp)
REVERT: a  234 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8877 (p0)
REVERT: a  294 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7522 (ttt-90)
REVERT: a  331 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8013 (m-10)
REVERT: a  341 LYS cc_start: 0.8197 (pttm) cc_final: 0.7909 (pttm)
REVERT: B   35 GLN cc_start: 0.8035 (mp10) cc_final: 0.7795 (mp10)
REVERT: B   67 MET cc_start: 0.8598 (tmm) cc_final: 0.8141 (tmm)
REVERT: B  156 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: B  234 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.9063 (p0)
REVERT: B  333 MET cc_start: 0.8141 (mtp) cc_final: 0.7607 (mtt)
REVERT: b   67 MET cc_start: 0.8572 (tmm) cc_final: 0.8022 (tmm)
REVERT: b  160 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6283 (t80)
REVERT: b  198 MET cc_start: 0.7905 (tpp) cc_final: 0.7631 (tpp)
  outliers start: 72
  outliers final: 47
  residues processed: 166
  average time/residue: 0.0838
  time to fit residues: 20.8793
Evaluate side-chains
  162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 106
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  188 ILE
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  241 MET
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  294 ARG
Chi-restraints excluded: chain a residue  297 SER
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  297 SER
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   61 THR
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  163 PHE
Chi-restraints excluded: chain b residue  188 ILE
Chi-restraints excluded: chain b residue  190 ASP
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  206 LEU
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  284 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Chi-restraints excluded: chain b residue  348 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 96 optimal weight:    0.4980
   chunk 122 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** a 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.152104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.093831 restraints weight = 15744.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098186 restraints weight = 8458.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.100913 restraints weight = 6009.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102626 restraints weight = 4953.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.103658 restraints weight = 4426.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11106  Z= 0.097
  Angle     :  0.496   6.067  15074  Z= 0.257
  Chirality :  0.039   0.144   1618
  Planarity :  0.003   0.023   1914
  Dihedral  :  6.343  57.248   1475
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 27.15 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.22), residues: 1346
  helix:  1.89 (0.45), residues: 154
  sheet: -1.43 (0.34), residues: 243
  loop : -1.64 (0.19), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.011   0.001   TYR A 113 
 PHE   0.009   0.001   PHE a 160 
 TRP   0.009   0.001   TRP B 225 
 HIS   0.007   0.001   HIS B 129 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 (11086)
  covalent geometry    : angle       0.49491 /  0.26 (15034)
  SS BOND              : bond        0.00217 /  0.14 (   20)
  SS BOND              : angle       0.71575 /  0.42 (   40)
  hydrogen bonds       : bond        0.03503 /  2.22 (  231)
  hydrogen bonds       : angle       5.22700 /  3.77 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 114
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8589 (ttp) cc_final: 0.7346 (tmm)
REVERT: A  160 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5367 (t80)
REVERT: A  275 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8125 (ttm)
REVERT: a   67 MET cc_start: 0.8590 (tmm) cc_final: 0.7762 (tmm)
REVERT: a   71 ILE cc_start: 0.7174 (tt) cc_final: 0.6723 (tt)
REVERT: a   89 MET cc_start: 0.7462 (mpp) cc_final: 0.6921 (mpp)
REVERT: a  154 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7042 (mm-30)
REVERT: a  206 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8553 (tp)
REVERT: a  234 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8895 (p0)
REVERT: a  331 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7944 (m-10)
REVERT: a  341 LYS cc_start: 0.8187 (pttm) cc_final: 0.7924 (pttm)
REVERT: B   35 GLN cc_start: 0.7947 (mp10) cc_final: 0.7623 (mp10)
REVERT: B   67 MET cc_start: 0.8465 (tmm) cc_final: 0.8032 (tmm)
REVERT: B   86 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8409 (mm)
REVERT: B  156 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: B  234 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9057 (p0)
REVERT: B  333 MET cc_start: 0.8052 (mtp) cc_final: 0.7575 (mtt)
REVERT: b   32 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6756 (m-80)
REVERT: b   67 MET cc_start: 0.8535 (tmm) cc_final: 0.7972 (tmm)
REVERT: b  160 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6066 (t80)
REVERT: b  234 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8440 (p0)
  outliers start: 61
  outliers final: 38
  residues processed: 164
  average time/residue: 0.0896
  time to fit residues: 22.2846
Evaluate side-chains
  154 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 105
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  275 MET
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  241 MET
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  297 SER
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  163 PHE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  234 ASN
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Chi-restraints excluded: chain b residue  348 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 121 optimal weight:    0.3980
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 123 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 67 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 110 optimal weight:   30.0000
   chunk 81 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
a 166 ASN
** a 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.147939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.089562 restraints weight = 15835.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.093728 restraints weight = 8508.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.096327 restraints weight = 6078.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097863 restraints weight = 5016.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.098862 restraints weight = 4507.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11106  Z= 0.212
  Angle     :  0.572   7.681  15074  Z= 0.298
  Chirality :  0.041   0.157   1618
  Planarity :  0.003   0.034   1914
  Dihedral  :  6.573  56.460   1471
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.73 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 26.22 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.90 (0.22), residues: 1346
  helix:  1.53 (0.43), residues: 160
  sheet: -1.57 (0.35), residues: 226
  loop : -1.80 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 257 
 TYR   0.012   0.002   TYR A 113 
 PHE   0.013   0.001   PHE a 217 
 TRP   0.014   0.001   TRP B 225 
 HIS   0.006   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00499 /  0.21 (11086)
  covalent geometry    : angle       0.57084 /  0.30 (15034)
  SS BOND              : bond        0.00346 /  0.23 (   20)
  SS BOND              : angle       0.84009 /  0.53 (   40)
  hydrogen bonds       : bond        0.04292 /  2.68 (  231)
  hydrogen bonds       : angle       5.51376 /  3.94 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 108
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7868 (m-80) cc_final: 0.7369 (m-80)
REVERT: A   67 MET cc_start: 0.8824 (ttp) cc_final: 0.7560 (tmm)
REVERT: A  160 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.5624 (t80)
REVERT: A  240 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8341 (mm-30)
REVERT: a   67 MET cc_start: 0.8716 (tmm) cc_final: 0.7826 (tmm)
REVERT: a   71 ILE cc_start: 0.7155 (tt) cc_final: 0.6693 (tt)
REVERT: a   89 MET cc_start: 0.7377 (mpp) cc_final: 0.6921 (mpp)
REVERT: a  154 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6356 (mp0)
REVERT: a  206 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8677 (tp)
REVERT: a  234 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9011 (p0)
REVERT: a  331 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8076 (m-10)
REVERT: B   35 GLN cc_start: 0.8249 (mp10) cc_final: 0.7949 (mp10)
REVERT: B   67 MET cc_start: 0.8578 (tmm) cc_final: 0.8127 (tmm)
REVERT: B   86 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (mm)
REVERT: B  156 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: B  234 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.9075 (p0)
REVERT: B  333 MET cc_start: 0.8122 (mtp) cc_final: 0.7606 (mtt)
REVERT: b   42 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8885 (mp)
REVERT: b   67 MET cc_start: 0.8556 (tmm) cc_final: 0.8008 (tmm)
REVERT: b  160 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6176 (t80)
REVERT: b  198 MET cc_start: 0.7816 (tpp) cc_final: 0.7430 (tpp)
REVERT: b  234 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8413 (p0)
  outliers start: 77
  outliers final: 53
  residues processed: 173
  average time/residue: 0.0874
  time to fit residues: 23.0839
Evaluate side-chains
  168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 104
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  172 LYS
Chi-restraints excluded: chain a residue  177 VAL
Chi-restraints excluded: chain a residue  188 ILE
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  241 MET
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  297 SER
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  297 SER
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   42 LEU
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   60 VAL
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  188 ILE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  206 LEU
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  234 ASN
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  284 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Chi-restraints excluded: chain b residue  348 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 90 optimal weight:    0.0370
   chunk 76 optimal weight:    4.9990
   chunk 108 optimal weight:    0.7980
   chunk 29 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.7664

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

Flipped N/Q/H residues before XYZ refinement:
** a 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 ASN
B 107 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.148805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.091037 restraints weight = 15859.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.095195 restraints weight = 8591.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.097857 restraints weight = 6121.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.099384 restraints weight = 5044.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.100394 restraints weight = 4542.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11106  Z= 0.163
  Angle     :  0.545   6.786  15074  Z= 0.284
  Chirality :  0.040   0.151   1618
  Planarity :  0.003   0.031   1914
  Dihedral  :  6.470  56.988   1469
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.25 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 27.66 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.22), residues: 1346
  helix:  1.61 (0.43), residues: 160
  sheet: -1.53 (0.35), residues: 231
  loop : -1.77 (0.18), residues: 955

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.012   0.001   TYR A 113 
 PHE   0.010   0.001   PHE a 217 
 TRP   0.014   0.001   TRP B 225 
 HIS   0.006   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.16 (11086)
  covalent geometry    : angle       0.54457 /  0.28 (15034)
  SS BOND              : bond        0.00272 /  0.18 (   20)
  SS BOND              : angle       0.75121 /  0.47 (   40)
  hydrogen bonds       : bond        0.03905 /  2.45 (  231)
  hydrogen bonds       : angle       5.38891 /  3.86 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 105
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7859 (m-80) cc_final: 0.7417 (m-80)
REVERT: A   67 MET cc_start: 0.8766 (ttp) cc_final: 0.7878 (tmm)
REVERT: A  160 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5507 (t80)
REVERT: A  240 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8542 (mm-30)
REVERT: a   67 MET cc_start: 0.8687 (tmm) cc_final: 0.7913 (tmm)
REVERT: a   71 ILE cc_start: 0.7402 (tt) cc_final: 0.7060 (tt)
REVERT: a   89 MET cc_start: 0.7463 (mpp) cc_final: 0.6949 (mpp)
REVERT: a  154 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7035 (mm-30)
REVERT: a  206 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8686 (tp)
REVERT: a  234 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.9026 (p0)
REVERT: a  331 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.7820 (m-10)
REVERT: B   35 GLN cc_start: 0.8389 (mp10) cc_final: 0.8150 (mp10)
REVERT: B   67 MET cc_start: 0.8571 (tmm) cc_final: 0.8132 (tmm)
REVERT: B   86 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8413 (mm)
REVERT: B  156 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8122 (tm-30)
REVERT: B  234 ASN cc_start: 0.9406 (OUTLIER) cc_final: 0.9116 (p0)
REVERT: B  333 MET cc_start: 0.8044 (mtp) cc_final: 0.7520 (mtt)
REVERT: b   32 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6870 (m-80)
REVERT: b   67 MET cc_start: 0.8636 (tmm) cc_final: 0.8055 (tmm)
REVERT: b  160 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6135 (t80)
REVERT: b  168 TRP cc_start: 0.8741 (m100) cc_final: 0.8028 (m100)
REVERT: b  198 MET cc_start: 0.8003 (tpp) cc_final: 0.7597 (tpp)
  outliers start: 69
  outliers final: 49
  residues processed: 164
  average time/residue: 0.0866
  time to fit residues: 21.7980
Evaluate side-chains
  161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 102
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue   28 TRP
Chi-restraints excluded: chain a residue   42 LEU
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  177 VAL
Chi-restraints excluded: chain a residue  184 MET
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  241 MET
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  297 SER
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  206 LEU
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Chi-restraints excluded: chain b residue  348 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0470
   chunk 126 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
a 263 GLN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.152356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095512 restraints weight = 15326.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.099710 restraints weight = 8315.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102391 restraints weight = 5938.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.104074 restraints weight = 4887.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.105044 restraints weight = 4357.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11106  Z= 0.091
  Angle     :  0.515   7.619  15074  Z= 0.266
  Chirality :  0.039   0.138   1618
  Planarity :  0.003   0.026   1914
  Dihedral  :  6.070  57.878   1469
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.50 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 29.09 %
    Favored  : 66.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.60 (0.22), residues: 1346
  helix:  1.85 (0.44), residues: 160
  sheet: -1.37 (0.35), residues: 245
  loop : -1.60 (0.19), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.012   0.001   TYR B 323 
 PHE   0.006   0.001   PHE b 217 
 TRP   0.009   0.001   TRP a 225 
 HIS   0.006   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.09 (11086)
  covalent geometry    : angle       0.51501 /  0.27 (15034)
  SS BOND              : bond        0.00199 /  0.13 (   20)
  SS BOND              : angle       0.61693 /  0.38 (   40)
  hydrogen bonds       : bond        0.03097 /  1.97 (  231)
  hydrogen bonds       : angle       4.98923 /  3.62 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 112
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8805 (ttp) cc_final: 0.7518 (tmm)
REVERT: A  160 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5690 (t80)
REVERT: a   67 MET cc_start: 0.8691 (tmm) cc_final: 0.7925 (tmm)
REVERT: a   71 ILE cc_start: 0.7277 (tt) cc_final: 0.6835 (tt)
REVERT: a   89 MET cc_start: 0.7760 (mpp) cc_final: 0.7204 (mpp)
REVERT: a  154 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7149 (mm-30)
REVERT: a  190 ASP cc_start: 0.7948 (p0) cc_final: 0.7590 (p0)
REVERT: a  206 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8691 (tp)
REVERT: a  234 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8859 (p0)
REVERT: a  331 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.7669 (m-10)
REVERT: a  341 LYS cc_start: 0.8184 (pttm) cc_final: 0.7929 (pttm)
REVERT: B   67 MET cc_start: 0.8570 (tmm) cc_final: 0.8134 (tmm)
REVERT: B   86 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8415 (mm)
REVERT: B  156 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: B  234 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9196 (p0)
REVERT: B  333 MET cc_start: 0.8081 (mtp) cc_final: 0.7637 (mtt)
REVERT: b   32 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6991 (m-80)
REVERT: b  160 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6202 (t80)
REVERT: b  168 TRP cc_start: 0.8681 (m100) cc_final: 0.7999 (m100)
  outliers start: 53
  outliers final: 34
  residues processed: 156
  average time/residue: 0.0859
  time to fit residues: 20.2185
Evaluate side-chains
  152 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 109
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  172 LYS
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   85 LYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  329 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    0.0770
   chunk 88 optimal weight:    0.4980
   chunk 115 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 129 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 82 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.153769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.095145 restraints weight = 15640.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.099389 restraints weight = 8518.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.102113 restraints weight = 6113.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103774 restraints weight = 5045.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.104681 restraints weight = 4522.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11106  Z= 0.095
  Angle     :  0.524   8.773  15074  Z= 0.269
  Chirality :  0.039   0.140   1618
  Planarity :  0.003   0.024   1914
  Dihedral  :  6.026  59.787   1466
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.13 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 29.93 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.22), residues: 1346
  helix:  1.87 (0.44), residues: 160
  sheet: -1.26 (0.36), residues: 236
  loop : -1.57 (0.19), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b 174 
 TYR   0.010   0.001   TYR A 323 
 PHE   0.006   0.001   PHE a 217 
 TRP   0.008   0.001   TRP B 225 
 HIS   0.005   0.001   HIS b  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.09 (11086)
  covalent geometry    : angle       0.52383 /  0.27 (15034)
  SS BOND              : bond        0.00200 /  0.13 (   20)
  SS BOND              : angle       0.58084 /  0.35 (   40)
  hydrogen bonds       : bond        0.03109 /  1.97 (  231)
  hydrogen bonds       : angle       4.88207 /  3.54 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 109
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8804 (ttp) cc_final: 0.7546 (tmm)
REVERT: A  160 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5696 (t80)
REVERT: A  174 ARG cc_start: 0.8073 (mmp80) cc_final: 0.7782 (mmp80)
REVERT: A  240 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8554 (mm-30)
REVERT: a   67 MET cc_start: 0.8704 (tmm) cc_final: 0.7597 (tmm)
REVERT: a   71 ILE cc_start: 0.7302 (tt) cc_final: 0.6923 (tt)
REVERT: a   89 MET cc_start: 0.7614 (mpp) cc_final: 0.7036 (mpp)
REVERT: a  154 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7110 (mm-30)
REVERT: a  234 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8835 (p0)
REVERT: a  331 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.7633 (m-10)
REVERT: a  341 LYS cc_start: 0.8226 (pttm) cc_final: 0.7982 (pttm)
REVERT: B   67 MET cc_start: 0.8688 (tmm) cc_final: 0.8245 (tmm)
REVERT: B   86 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8374 (mm)
REVERT: B  156 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: B  234 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9214 (p0)
REVERT: B  333 MET cc_start: 0.8059 (mtp) cc_final: 0.7659 (mtt)
REVERT: b   32 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6941 (m-80)
REVERT: b  160 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6182 (t80)
REVERT: b  168 TRP cc_start: 0.8658 (m100) cc_final: 0.8007 (m100)
REVERT: b  174 ARG cc_start: 0.7937 (mmp80) cc_final: 0.7677 (mmp80)
  outliers start: 52
  outliers final: 37
  residues processed: 153
  average time/residue: 0.0907
  time to fit residues: 20.9146
Evaluate side-chains
  152 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 106
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  172 LYS
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   85 LYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  212 ILE
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  318 LEU
Chi-restraints excluded: chain b residue  329 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 75 optimal weight:    0.0970
   chunk 54 optimal weight:    0.0040
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.9394

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.151777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.094016 restraints weight = 15602.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.098105 restraints weight = 8815.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.100672 restraints weight = 6426.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102263 restraints weight = 5352.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.103119 restraints weight = 4815.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11106  Z= 0.112
  Angle     :  0.539  10.893  15074  Z= 0.276
  Chirality :  0.040   0.156   1618
  Planarity :  0.002   0.025   1914
  Dihedral  :  5.990  58.557   1466
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.95 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 29.51 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.51 (0.22), residues: 1346
  helix:  1.84 (0.44), residues: 160
  sheet: -1.18 (0.37), residues: 230
  loop : -1.56 (0.19), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b 174 
 TYR   0.019   0.001   TYR A 323 
 PHE   0.007   0.001   PHE a 217 
 TRP   0.008   0.001   TRP B 225 
 HIS   0.007   0.001   HIS B  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.11 (11086)
  covalent geometry    : angle       0.53908 /  0.28 (15034)
  SS BOND              : bond        0.00206 /  0.13 (   20)
  SS BOND              : angle       0.61107 /  0.38 (   40)
  hydrogen bonds       : bond        0.03314 /  2.09 (  231)
  hydrogen bonds       : angle       4.93658 /  3.56 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 106
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8772 (ttp) cc_final: 0.7514 (tmm)
REVERT: A  160 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5665 (t80)
REVERT: A  240 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8522 (mm-30)
REVERT: a   67 MET cc_start: 0.8717 (tmm) cc_final: 0.7946 (tmm)
REVERT: a   71 ILE cc_start: 0.7320 (tt) cc_final: 0.6987 (tt)
REVERT: a   89 MET cc_start: 0.7592 (mpp) cc_final: 0.7015 (mpp)
REVERT: a  154 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7061 (mm-30)
REVERT: a  206 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8659 (tp)
REVERT: a  234 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8823 (p0)
REVERT: a  331 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.7712 (m-10)
REVERT: a  341 LYS cc_start: 0.8152 (pttm) cc_final: 0.7901 (pttm)
REVERT: B   67 MET cc_start: 0.8595 (tmm) cc_final: 0.8160 (tmm)
REVERT: B   86 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8383 (mm)
REVERT: B  156 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: B  234 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.9196 (p0)
REVERT: B  333 MET cc_start: 0.8074 (mtp) cc_final: 0.7637 (mtt)
REVERT: b   32 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6917 (m-80)
REVERT: b  160 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6289 (t80)
REVERT: b  168 TRP cc_start: 0.8648 (m100) cc_final: 0.7921 (m100)
  outliers start: 55
  outliers final: 38
  residues processed: 151
  average time/residue: 0.0871
  time to fit residues: 20.0807
Evaluate side-chains
  153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue   42 LEU
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   85 LYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  318 LEU
Chi-restraints excluded: chain b residue  329 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 109 optimal weight:    0.0020
   chunk 24 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 66 optimal weight:    0.3980
   chunk 123 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.154144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.097383 restraints weight = 15418.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.101626 restraints weight = 8422.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104360 restraints weight = 6008.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.106028 restraints weight = 4955.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.106895 restraints weight = 4431.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11106  Z= 0.094
  Angle     :  0.535  11.565  15074  Z= 0.272
  Chirality :  0.039   0.146   1618
  Planarity :  0.003   0.031   1914
  Dihedral  :  5.865  56.890   1466
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.54 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 30.02 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.41 (0.23), residues: 1346
  helix:  1.92 (0.44), residues: 160
  sheet: -1.38 (0.36), residues: 244
  loop : -1.41 (0.19), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG b 174 
 TYR   0.016   0.001   TYR B 323 
 PHE   0.006   0.001   PHE A 217 
 TRP   0.007   0.001   TRP B 225 
 HIS   0.006   0.001   HIS B  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.09 (11086)
  covalent geometry    : angle       0.53492 /  0.27 (15034)
  SS BOND              : bond        0.00173 /  0.11 (   20)
  SS BOND              : angle       0.56624 /  0.34 (   40)
  hydrogen bonds       : bond        0.03042 /  1.93 (  231)
  hydrogen bonds       : angle       4.82129 /  3.48 (  582)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8783 (ttp) cc_final: 0.7532 (tmm)
REVERT: A  160 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5757 (t80)
REVERT: A  174 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7635 (mmp80)
REVERT: a   67 MET cc_start: 0.8686 (tmm) cc_final: 0.7573 (tmm)
REVERT: a   71 ILE cc_start: 0.7278 (tt) cc_final: 0.6909 (tt)
REVERT: a   89 MET cc_start: 0.7635 (mpp) cc_final: 0.7050 (mpp)
REVERT: a  154 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7095 (mm-30)
REVERT: a  206 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8618 (tp)
REVERT: a  234 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8959 (p0)
REVERT: a  331 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7735 (m-10)
REVERT: a  341 LYS cc_start: 0.8324 (pttm) cc_final: 0.8115 (pttm)
REVERT: B   67 MET cc_start: 0.8692 (tmm) cc_final: 0.8248 (tmm)
REVERT: B   86 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8343 (mm)
REVERT: B  156 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: B  234 ASN cc_start: 0.9434 (OUTLIER) cc_final: 0.9206 (p0)
REVERT: B  333 MET cc_start: 0.7887 (mtp) cc_final: 0.7463 (mtt)
REVERT: b   32 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6970 (m-80)
REVERT: b  160 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6404 (t80)
REVERT: b  168 TRP cc_start: 0.8635 (m100) cc_final: 0.7958 (m100)
  outliers start: 48
  outliers final: 37
  residues processed: 149
  average time/residue: 0.0869
  time to fit residues: 19.9556
Evaluate side-chains
  153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 107
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 TYR
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  158 TYR
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain a residue  133 PHE
Chi-restraints excluded: chain a residue  135 ILE
Chi-restraints excluded: chain a residue  154 GLU
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  209 THR
Chi-restraints excluded: chain a residue  234 ASN
Chi-restraints excluded: chain a residue  283 THR
Chi-restraints excluded: chain a residue  300 THR
Chi-restraints excluded: chain a residue  331 TYR
Chi-restraints excluded: chain a residue  346 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   85 LYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain b residue   28 TRP
Chi-restraints excluded: chain b residue   32 TYR
Chi-restraints excluded: chain b residue   59 SER
Chi-restraints excluded: chain b residue   63 LEU
Chi-restraints excluded: chain b residue  160 PHE
Chi-restraints excluded: chain b residue  194 VAL
Chi-restraints excluded: chain b residue  209 THR
Chi-restraints excluded: chain b residue  264 THR
Chi-restraints excluded: chain b residue  283 THR
Chi-restraints excluded: chain b residue  286 VAL
Chi-restraints excluded: chain b residue  318 LEU
Chi-restraints excluded: chain b residue  329 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 109 optimal weight:    0.2980
   chunk 47 optimal weight:    0.0670
   chunk 48 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 195 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.157447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.097161 restraints weight = 15844.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.101876 restraints weight = 8284.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.104891 restraints weight = 5864.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.106717 restraints weight = 4813.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.107619 restraints weight = 4318.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
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      :  0.002   0.041  11106  Z= 0.096
  Angle     :  0.535  11.741  15074  Z= 0.272
  Chirality :  0.039   0.140   1618
  Planarity :  0.002   0.024   1914
  Dihedral  :  5.840  56.778   1466
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.73 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 29.85 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.23), residues: 1346
  helix:  1.90 (0.44), residues: 160
  sheet: -1.37 (0.36), residues: 245
  loop : -1.38 (0.19), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b 174 
 TYR   0.014   0.001   TYR A 323 
 PHE   0.032   0.001   PHE B 163 
 TRP   0.007   0.001   TRP B 225 
 HIS   0.006   0.001   HIS B  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.10 (11086)
  covalent geometry    : angle       0.53515 /  0.27 (15034)
  SS BOND              : bond        0.00181 /  0.12 (   20)
  SS BOND              : angle       0.56222 /  0.34 (   40)
  hydrogen bonds       : bond        0.03079 /  1.94 (  231)
  hydrogen bonds       : angle       4.78016 /  3.45 (  582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1980.25 seconds
wall clock time: 34 minutes 54.39 seconds (2094.39 seconds total)